[gmx-users] Help regarding running DSSP in gmx

Mon Mar 19 14:45:54 CET 2012

Hi Chandran,

What did you try, and what error did it come up with? What platform
are you using, and which version of DSSP? The latest version of DSSP
won't work with Gromacs yet.

Cheers,

Tsjerk

On Mon, Mar 19, 2012 at 2:39 PM, chandran karunakaran
<ckaru2000 at yahoo.com> wrote:
> 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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> Subject: gmx-users Digest, Vol 95, Issue 125
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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)
>
>
> ----------------------------------------------------------------------
>
> 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>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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>
> Message-ID:
>     <1332152362.73030.YahooMailNeo at web29401.mail.ird.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Hi
>
> in a topology file in the section [ moleculetypes ] is standing
>
> ; nrexcl
>
>     3
>
> What do this mean?
>
> Thanks for help
> Greetings
> Lara
>
>
> ------------------------------
>
> 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
> Message-ID:
>     <CAEuVTxAiRNq6nDxPPKgG_S34ufzYZVg2Z2-BkoAucNQOK4FtMQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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>
> Content-Type: text/plain; charset="utf-8"
>
>
> >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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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands