CCL: NAMD vs GROMACS?
- From: Andras Borosy <andras.borosy]^[givaudan.com>
- Subject: CCL: NAMD vs GROMACS?
- Date: Thu, 17 Jul 2014 15:23:01 +0200
Dear Vitaly,
As my complexes are not two large I chose NAMD (which can be started also
> from MOE directly :)
Do you happen to know how NAMD can be run parallel on multicore
processors?
Best regards,
Andras Borosy
> From: "Dr. Vitaly Chaban vvchaban%x%gmail.com"
<owner-chemistry+*+ccl.net>
To: "Borosy, Andras " <andras.borosy+*+givaudan.com>,
Date: 07/05/2014 12:34 AM
Subject: CCL: NAMD vs GROMACS?
Sent by: owner-chemistry+andras.borosy==givaudan.com+*+ccl.net
Sent to CCL by: "Dr. Vitaly Chaban" [vvchaban##gmail.com]
I believe NAMD is somewhat easier while gromacs is faster.
Dr. Vitaly V. Chaban
On Wed, Jul 2, 2014 at 10:20 AM, Andras Borosy
andras.borosy[]givaudan.com <owner-chemistry||ccl.net> wrote:
> Dear Colleagues,
>
> I wish to run MD simulations by using a relatively small host system
(with
> a small organic guest molecule) in batch mode at a parallel RedHat linux
> computer. NAMD vs GROMACS (or anything else) would be better for a
novice?
>
> Many thanks,
>
> Andras Borosyhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp-:-//www.ccl.net/chemistry/sub_unsub.shtmlhttp-:-//www.ccl.net/spammers.txt--=_alternative
0049847AC1257D18_=
Content-Type: text/html; charset="US-ASCII"
<br><font size=2 face="sans-serif">Dear
Vitaly,</font>
<br>
<br><font size=2 face="sans-serif">As my complexes are not
two large I
chose NAMD (which can be started also from MOE directly :)</font>
<br>
<br><font size=2 face="sans-serif">Do you happen to know
how NAMD
can be run parallel on multicore processors?</font>
<br>
<br><font size=2 face="sans-serif">Best
regards,</font>
<br>
<br><font size=2 face="sans-serif">Andras
Borosy</font>
<br>
<br>
<br>
<br><font size=1 color=#5f5f5f face="sans-serif">From:
</font><font size=1
face="sans-serif">"Dr. Vitaly Chaban
vvchaban%x%gmail.com"
<owner-chemistry+*+ccl.net></font>
<br><font size=1 color=#5f5f5f face="sans-serif">To:
</font><font size=1
face="sans-serif">"Borosy, Andras
" <andras.borosy+*+givaudan.com>, </font>
<br><font size=1 color=#5f5f5f face="sans-serif">Date:
</font><font size=1 face="sans-serif">07/05/2014
12:34 AM</font>
<br><font size=1 color=#5f5f5f face="sans-serif">Subject:
</font><font size=1
face="sans-serif">CCL: NAMD vs
GROMACS?</font>
<br><font size=1 color=#5f5f5f face="sans-serif">Sent by:
</font><font size=1
face="sans-serif">owner-chemistry+andras.borosy==givaudan.com+*+ccl.net</font>
<br>
<hr noshade>
<br>
<br>
<br><tt><font size=2><br>
Sent to CCL by: "Dr. Vitaly Chaban"
[vvchaban##gmail.com]<br>
I believe NAMD is somewhat easier while gromacs is faster.<br>
<br>
<br>
Dr. Vitaly V. Chaban<br>
<br>
<br>
On Wed, Jul 2, 2014 at 10:20 AM, Andras Borosy<br>
andras.borosy[]givaudan.com <owner-chemistry||ccl.net>
wrote:<br>
> Dear Colleagues,<br>
><br>
> I wish to run MD simulations by using a relatively small host
system (with<br>
> a small organic guest molecule) in batch mode at a parallel RedHat
linux<br>
> computer. NAMD vs GROMACS (or anything else) would be better for a
novice?<br>
><br>
> Many thanks,<br>
><br>
> Andras Borosy<br>
><br>
><br>
<br>
<br>
<br<br<br<br<br>
<br<br>
</font></tt><a href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message";><tt><font
size=2>http://www.ccl.net/cgi-bin/ccl/send_ccl_message</font></tt></a><tt><font
size=2><br>
<br<br>
</font></tt><a href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message";><tt><font
size=2>http://www.ccl.net/cgi-bin/ccl/send_ccl_message</font></tt></a><tt><font
size=2><br>
<br<br>
</font></tt><a href=http://www.ccl.net/chemistry/sub_unsub.shtml><tt><font
size=2>http://www.ccl.net/chemistry/sub_unsub.shtml</font></tt></a><tt><font
size=2><br>
<br>
Before posting, check wait time at: </font></tt><a href=http://www.ccl.net/><tt><font size=2>http://www.ccl.net</font></tt></a><tt><font
size=2><br>
<br>
Job: </font></tt><a href=http://www.ccl.net/jobs><tt><font size=2>http://www.ccl.net/jobs</font></tt></a><tt><font
size=2>
<br>
Conferences: </font></tt><a href=http://server.ccl.net/chemistry/announcements/conferences/><tt><font
size=2>http://server.ccl.net/chemistry/announcements/conferences/</font></tt></a><tt><font
size=2><br>
<br>
Search Messages: </font></tt><a href=http://www.ccl.net/chemistry/searchccl/index.shtml><tt><font
size=2>http://www.ccl.net/chemistry/searchccl/index.shtml</font></tt></a><tt><font
size=2><br>
<br<br>
</font></tt><a href=http://www.ccl.net/spammers.txt><tt><font size=2>http://www.ccl.net/spammers.txt</font></tt></a><tt><font
size=2><br>
<br>
RTFI: </font></tt><a href=http://www.ccl.net/chemistry/aboutccl/instructions/><tt><font
size=2>http://www.ccl.net/chemistry/aboutccl/instructions/</font></tt></a><tt><font
size=2><br>
<br>
<br>
</font></tt>
<br>