[gmx-users] Help regarding running DSSP in gmx
chandran karunakaran
ckaru2000 at yahoo.com
Mon Mar 19 14:39:10 CET 2012
Dear ALL,
We could not run DSSP for analysing the secondary structure. Any help in this regard is very much appreciated
*******************************+
Dr.Karunakaran Chandran +
Biophysics Department +
Medical College of Wisconsin +
Milwaukee, WI-53226 +
Resi.: 414-443-0085 +
Off : 414-456-4034 +
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Today's Topics:
1. Editing potential parameters (Asaf Farhi)
2. nrexcl in topology (Lara Bunte)
3. extending simulation (priya thiyagarajan)
4. Re: nrexcl in topology (R.Perez Garcia)
5. Re: Force constant - Umbrella Sampling (lloyd riggs)
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Message: 1
Date: Mon, 19 Mar 2012 10:06:47 +0000
From: Asaf Farhi <asaf.farhi at weizmann.ac.il>
Subject: [gmx-users] Editing potential parameters
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Message-ID: <7D02BCA1E8377E4AABC2E8F59B6D0CDA09E25B at IBWMBX01>
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Dear Gromacs user
Hi. My name is Asaf and I'm trying to edit potential parameters for the non bonded interaction potential terms between specific atoms (k1 for 1 subset of pairs and k2 for anoother subset of pairs).
Is the pairs section in the topology file the correct place to do this? and if so how would you incorporate spring constant for particular pair interaction?
Many thanks.
Best regards,
Asaf
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Message: 2
Date: Mon, 19 Mar 2012 10:19:22 +0000 (GMT)
From: Lara Bunte <lara.bunte at yahoo.de>
Subject: [gmx-users] nrexcl in topology
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
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<1332152362.73030.YahooMailNeo at web29401.mail.ird.yahoo.com>
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Hi
in a topology file in the section [ moleculetypes ] is standing
; nrexcl
3
What do this mean?
Thanks for help
Greetings
Lara
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Message: 3
Date: Mon, 19 Mar 2012 03:26:55 -0700
From: priya thiyagarajan <priya.thiyagarajan09 at gmail.com>
Subject: [gmx-users] extending simulation
To: gmx-users at gromacs.org
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<CAEuVTxAiRNq6nDxPPKgG_S34ufzYZVg2Z2-BkoAucNQOK4FtMQ at mail.gmail.com>
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hello sir,,
initially i did my simulation for 10ns.. after getting result i analysed it
and thought of extending the simulation for another 10ns..
i used following commands..
tpbconv *-s md.tpr -o newmd.tpr -extend 10000.00*
*mdrun -s newmd.tpr -o md3_2.trr -c md_2.gro -e md_2.edr -g md_2.log -cpi
state1.cpt -noappend*
is it correct..
we ll use tpbconv to extend the simulation which terminated in the middle..
is it correct to use the same command for completed run...
please help me with your answer..
Thanking you sir,
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Message: 4
Date: Mon, 19 Mar 2012 11:27:43 +0100
From: "R.Perez Garcia" <r.perez.garcia at student.rug.nl>
Subject: Re: [gmx-users] nrexcl in topology
To: Lara Bunte <lara.bunte at yahoo.de>, "gmx-users at gromacs.org"
<gmx-users at gromacs.org>
Message-ID: <7630868d774ff.4f67182f at rug.nl>
Content-Type: text/plain; charset="iso-8859-1"
http://lists.gromacs.org/pipermail/gmx-users/2011-May/061072.html
On 19-03-12, Lara Bunte <lara.bunte at yahoo.de> wrote:
> Hi
>
> in a topology file in the section [ moleculetypes ] is standing
>
> ; nrexcl
>
> 3
>
> What do this mean?
>
> Thanks for help
> Greetings
> Lara
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Message: 5
Date: Mon, 19 Mar 2012 11:43:49 +0100
From: "lloyd riggs" <lloyd.riggs at gmx.ch>
Subject: Re: [gmx-users] Force constant - Umbrella Sampling
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <20120319104349.106190 at gmx.net>
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>From liturature it ranges around 1K for unravling proteins, and protein-protein dissociations range around 2-3k (kj/mol that is). For small molecules I have no clue. Id like to know if somone finds out ranges for any of these though....
Stephan Watkins
-------- Original-Nachricht --------
> Datum: Mon, 19 Mar 2012 08:48:15 +0000
> Von: Steven Neumann <s.neumann08 at gmail.com>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>, jalemkul at vt.edu
> Betreff: [gmx-users] Force constant - Umbrella Sampling
> Dear Gmx Users, Dear Justin,
>
> As I saw in your tutorial you used the force of 1000 kJ/mol nm2 for the
> harmonic potential. You pulled the whole chain which is quite heavy. Would
> you decrease the force constant for a small molecule (app. 500 Da) during
> the umbrella sampling (e.g. 500 kJ/mol nm2) ? Is it a guess or I should
> check calculations for e.g. 3 force constants and see the influence on the
> final binding free energy?
>
> Thank you,
>
> Steven
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