From chemistry-request@server.ccl.net Mon Oct 28 02:22:46 2002
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Date: Mon, 28 Oct 2002 02:23:35 -0500
From: Joshua Speidel <joshua.speidel@mssm.edu>
Subject: CHARMM Temperature calculation..
To: CHEMISTRY@ccl.net
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Hi All,

I'm trying to calculate the average temperature of the water in my system
over the course of my simulation.  My procedure is this:

I generate my psf and read my starting coordinates in, and then I open my
velocity trajectory.   After that I use these commands:

CORREL MAXA 50000 INBF 0

ENTER WAT1 TEMP
TRAJ FIRSTU 13 NUNI 1 SELE RESN TIP3 end VELO

OPEN UNIT 60 CARD NAME "ALL_water_temp.txt" WRITE

WRITE WAT1 UNIT 60 CARD
* TEMPERATURE
*

and although I get no errors, the average temp is "inf" and the fluctuation
is 0.00.  I'm pretty sure that it's something simple that I'm missing, but
if you know either why what I'm doing isn't working, or a better way to
accomplish it, I would greatly appreciate your help.

Thanks!

Josh


From chemistry-request@server.ccl.net Mon Oct 28 05:33:01 2002
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Date: Mon, 28 Oct 2002 18:43:00 +0800
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Subject: Temperature Control in NAMD
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Dear all:
    I used temperature coupling to control temperature in NAMD. But when 
I set temperature for heat bath to 298K, I found after 2000-3000 steps 
the termerature could stabilize to 298K(I set inital temp. to 298K, 
during the simulation temp. increased to about 318K quickly and then 
decreased to 298K slowly). what's the matter? If I used it to do a 
equilibrate simulation(system is temperature sensitive), would the first 
few thousand steps have any  influence?

Chen Hao




From chemistry-request@server.ccl.net Mon Oct 28 03:09:22 2002
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From: "Tamas E. Gunda" <tamasgunda@tigris.klte.hu>
To: "Victor Ferro" <victor.ferro@uam.es>, <chemistry@ccl.net>
References: <5.0.2.1.1.20021025091218.02247bc0@pop.uam.es>
Subject: Re: CCL:Fwd: File convertion
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Please find the attached molfile in MDL's mol format; it was converted with
Mol2Mol
Tamas Gunda



----- Original Message -----
From: "Victor Ferro" <victor.ferro@uam.es>
To: <chemistry@ccl.net>
Sent: Friday, October 25, 2002 08:13
Subject: CCL:Fwd: File convertion


>
> >>>>Dear colleagues:
> >>>>I have attempted to convert the geometry contained in the attached
file
> >>>>to cartesian (or internal) coordinates using Babel, but I have not
> >>>>achieved to make it.
> >>>>Would someone help me, please.
> >>>>I will be very gratefully.
> >>>>Thank you in advance
> >>>>
> >>>>Victor Ferro.
>

---------------cut here--------------
CSD_CIF_PHTLBC
  Mol2Mol 10280209083D

 44 52  0  0  0  0  0  0  0  0999 V2000
    3.5217    3.7060    0.6113 B   0  0  0  0  0  0  0  0  0
    3.8042    3.7060    2.4534 Cl  0  0  0  0  0  0  0  0  0
    5.3002    2.5586   -0.7078 C   0  0  0  0  0  0  0  0  0
    0.0388    2.9870   -0.3477 C   0  0  0  0  0  0  0  0  0
   -1.1238    2.2844   -0.6974 C   0  0  0  0  0  0  0  0  0
   -2.2367    3.0019   -0.9776 C   0  0  0  0  0  0  0  0  0
    5.5002    1.2230   -1.2485 C   0  0  0  0  0  0  0  0  0
    6.5307    0.6434   -1.9687 C   0  0  0  0  0  0  0  0  0
    6.3864   -0.6656   -2.3703 C   0  0  0  0  0  0  0  0  0
    5.2165   -1.3727   -2.1379 C   0  0  0  0  0  0  0  0  0
    4.1461   -0.7872   -1.4944 C   0  0  0  0  0  0  0  0  0
    4.2891    0.5114   -1.0326 C   0  0  0  0  0  0  0  0  0
    3.3605    1.4157   -0.3529 C   0  0  0  0  0  0  0  0  0
    1.4099    2.5631   -0.0602 C   0  0  0  0  0  0  0  0  0
    7.4193    1.2452   -2.1067 H   0  0  0  0  0  0  0  0  0
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   -1.1638    1.3045   -0.7161 H   0  0  0  0  0  0  0  0  0
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    7.4193    6.1668   -2.1067 H   0  0  0  0  0  0  0  0  0
    5.2165    8.7847   -2.1379 C   0  0  0  0  0  0  0  0  0
    3.3459    8.7313   -1.2350 H   0  0  0  0  0  0  0  0  0
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    5.1523    9.8135   -2.3454 H   0  0  0  0  0  0  0  0  0
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 39 43  1  0  0  0  0
 41 44  1  0  0  0  0
  1 25  1  0  0  0  0
M  END
----------cut here-----------

------=_NextPart_000_001F_01C27E62.2418B910
Content-Type: chemical/x-mdl-molfile;
	name="subPc-rX.MOL"
Content-Transfer-Encoding: 7bit
Content-Disposition: attachment;
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CSD_CIF_PHTLBC
  Mol2Mol 10280209083D

 44 52  0  0  0  0  0  0  0  0999 V2000
    3.5217    3.7060    0.6113 B   0  0  0  0  0  0  0  0  0
    3.8042    3.7060    2.4534 Cl  0  0  0  0  0  0  0  0  0
    5.3002    2.5586   -0.7078 C   0  0  0  0  0  0  0  0  0
    0.0388    2.9870   -0.3477 C   0  0  0  0  0  0  0  0  0
   -1.1238    2.2844   -0.6974 C   0  0  0  0  0  0  0  0  0
   -2.2367    3.0019   -0.9776 C   0  0  0  0  0  0  0  0  0
    5.5002    1.2230   -1.2485 C   0  0  0  0  0  0  0  0  0
    6.5307    0.6434   -1.9687 C   0  0  0  0  0  0  0  0  0
    6.3864   -0.6656   -2.3703 C   0  0  0  0  0  0  0  0  0
    5.2165   -1.3727   -2.1379 C   0  0  0  0  0  0  0  0  0
    4.1461   -0.7872   -1.4944 C   0  0  0  0  0  0  0  0  0
    4.2891    0.5114   -1.0326 C   0  0  0  0  0  0  0  0  0
    3.3605    1.4157   -0.3529 C   0  0  0  0  0  0  0  0  0
    1.4099    2.5631   -0.0602 C   0  0  0  0  0  0  0  0  0
    7.4193    1.2452   -2.1067 H   0  0  0  0  0  0  0  0  0
    7.1162   -1.0822   -2.9681 H   0  0  0  0  0  0  0  0  0
    5.1523   -2.4015   -2.3454 H   0  0  0  0  0  0  0  0  0
    3.3459   -1.3193   -1.2350 H   0  0  0  0  0  0  0  0  0
   -1.1638    1.3045   -0.7161 H   0  0  0  0  0  0  0  0  0
   -3.2005    2.6683   -1.5671 H   0  0  0  0  0  0  0  0  0
    5.9657    3.7060   -0.9548 N   0  0  0  0  0  0  0  0  0
    4.0915    2.5423   -0.0737 N   0  0  0  0  0  0  0  0  0
    2.0245    1.3875   -0.2864 N   0  0  0  0  0  0  0  0  0
    2.0973    3.7060    0.2563 N   0  0  0  0  0  0  0  0  0
    4.0915    4.8697   -0.0737 N   0  0  0  0  0  0  0  0  0
    5.3002    4.8534   -0.7078 C   0  0  0  0  0  0  0  0  0
    0.0388    4.4250   -0.3477 C   0  0  0  0  0  0  0  0  0
   -2.2367    4.4101   -0.9776 C   0  0  0  0  0  0  0  0  0
    1.4099    4.8489   -0.0602 C   0  0  0  0  0  0  0  0  0
    3.3605    5.9963   -0.3529 C   0  0  0  0  0  0  0  0  0
    5.5002    6.1890   -1.2485 C   0  0  0  0  0  0  0  0  0
   -1.1238    5.1276   -0.6974 C   0  0  0  0  0  0  0  0  0
   -3.2005    4.7437   -1.5671 H   0  0  0  0  0  0  0  0  0
    2.0245    6.0245   -0.2864 N   0  0  0  0  0  0  0  0  0
    4.2891    6.9006   -1.0326 C   0  0  0  0  0  0  0  0  0
    6.5307    6.7686   -1.9687 C   0  0  0  0  0  0  0  0  0
   -1.1638    6.1075   -0.7161 H   0  0  0  0  0  0  0  0  0
    4.1461    8.1992   -1.4944 C   0  0  0  0  0  0  0  0  0
    6.3864    8.0776   -2.3703 C   0  0  0  0  0  0  0  0  0
    7.4193    6.1668   -2.1067 H   0  0  0  0  0  0  0  0  0
    5.2165    8.7847   -2.1379 C   0  0  0  0  0  0  0  0  0
    3.3459    8.7313   -1.2350 H   0  0  0  0  0  0  0  0  0
    7.1162    8.4942   -2.9681 H   0  0  0  0  0  0  0  0  0
    5.1523    9.8135   -2.3454 H   0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 22  1  0  0  0  0
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 25 26  1  0  0  0  0
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 26 31  1  0  0  0  0
 27 29  1  0  0  0  0
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M  END

------=_NextPart_000_001F_01C27E62.2418B910--



From chemistry-request@server.ccl.net Mon Oct 28 14:05:39 2002
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Date: Mon, 28 Oct 2002 19:05:22 +0000
From: Luca Fenu <l.a.fenu@soton.ac.uk>
Organization: university of southampton
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Subject: CCL: scripting pymol
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Dear all,

I need to scan and make a choice about a list of molecules. does anyone
knows how to send command to pymol through a perl or shell script? I've
read pymol's manual, and it's possible to pass pymol some scripts, from
its internal shell. but I don't know how to pass commands to it from
another program. starting the process in foreground and feeding the
command from the stdout of perl to the stdin of pymol doesn't work. I
think pymol use another filehandle for aquiring commands. how can I
avoid to restar a new pymol for every molecule?
any suggestion? many thanks

	luca


-- 
Universities are places of knowledge.  The freshman each bring a little
in with them, and the seniors take none away, so knowledge accumulates.

From chemistry-request@server.ccl.net Mon Oct 28 14:26:36 2002
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Subject: Gaussian input file -- molecule specification
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Hi --

I was wondering what units the molecule specification is in when
cartesian coordinates are used.  is it in bohrs?  or angstroms?

thank you,
connie chang


From chemistry-request@server.ccl.net Mon Oct 28 14:53:34 2002
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Date: Mon, 28 Oct 2002 13:53:13 -0600 (CST)
From: Jim Phillips <jim@ks.uiuc.edu>
To: Chen Hao <kzong@263.sina.com>
cc: chemistry@server.ccl.net
Subject: Re: CCL:Temperature Control in NAMD
In-Reply-To: <3DBD14B4.3030303@263.sina.com>
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Hi,

This sounds like your system wasn't minimized at the beginning of the
simulation, and you are seeing the initial conversion of potential to
kinetic energy.  You should generally ignore the initial equilibration
period during analysis.

-Jim


On Mon, 28 Oct 2002, Chen Hao wrote:

> Dear all:
>     I used temperature coupling to control temperature in NAMD. But when
> I set temperature for heat bath to 298K, I found after 2000-3000 steps
> the termerature could stabilize to 298K(I set inital temp. to 298K,
> during the simulation temp. increased to about 318K quickly and then
> decreased to 298K slowly). what's the matter? If I used it to do a
> equilibrate simulation(system is temperature sensitive), would the first
> few thousand steps have any  influence?
>
> Chen Hao
>
>
>
>
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From chemistry-request@server.ccl.net Mon Oct 28 15:54:28 2002
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Message-ID: <008601c27ec4$5d8f5700$cf021dac@winlinux>
From: "Minh Tung" <tung092@chemdep.hcmuns.edu.vn>
To: <chemistry@ccl.net>
Subject: Gaussian in Linux
Date: Tue, 29 Oct 2002 03:55:36 +0700
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Dear All
I'm starting using Gaussian on Linux Redhat but I don't know what is the
best program to model molecular on it. Is there any free software to
modeling and give Gaussian input like GaussView on Windows ?. And on Linux
Redhat, why it use memory resource too much ? how I control it ?
Best regrad.

Minh Tung
tung092@chemdep.hcmuns.edu.vn
Natural Science University
Viet Nam



