[gmx-users] Thymine-TOP and Force field parameters

Tue Apr 5 14:15:53 CEST 2005

Hi

GMXFF isn't aware of DNA, I guess. You also shouldn't use it.
Use AMBER to get an amber topology file and convert it to GROMACS, or 
use the new OPLSAAFF, which includes DNA parameters. But this is still 
in testing phase, when I remember correctly.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

chandran karunakaran wrote:
> Dear GMX users,
> 
>   I could not find topology and force
> field parameters for thymine residue
> in the ffgmx.rtp. But there is force
> field and topology for DTHY. What does
> DTHY mean? Can we use the force field
> and topology for THYMINE residue of DNA.
> Thank you so much in advance.
> 
> With thanks
> Dr.C.Karunakaran
> 
>   
> --- gmx-users-request at gromacs.org wrote:
> 
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>>Today's Topics:
>>
>>   1. gen_seed (herbst at fhi-berlin.mpg.de)
>>   2. Re: gen_seed (David van der Spoel)
>>   3. total time for MDsimulation (shailza singh)
>>   4. g_cluster (Hendrik Preuss)
>>   5. Re: total time for MDsimulation (Maik Goette)
>>   6. Re: Topology for hetroatom (PRODRG) (Alok)
>>   7. Re: Topology for hetroatom (PRODRG) (David)
>>   8. file truncated (shailza singh)
>>
>>
>>
> 
> ----------------------------------------------------------------------
> 
>>Message: 1
>>Date: Wed, 23 Feb 2005 14:26:55 +0100 (CET)
>>From: herbst at fhi-berlin.mpg.de
>>Subject: [gmx-users] gen_seed
>>To: gmx-users at gromacs.org
>>Message-ID:
>>
> 
> <44137.141.14.132.138.1109165215.squirrel at 141.14.132.138>
> 
>>Content-Type: text/plain;charset=iso-8859-1
>>
>>Hello all!
>>
>>I want to run two different simulations with the
>>same system and have a
>>question concerning gen_seed.
>>Is it ok when I use values like 7 and 13 for the two
>>simulations, or are
>>these
>>values too close together and I will get nearly
>>identical velocity
>>distributions?
>>How far apart should I chose the two gen_seeds?
>>
>>Thanks,
>>Anna
>>
>>
>>------------------------------
>>
>>Message: 2
>>Date: Wed, 23 Feb 2005 14:50:42 +0100
>>From: David van der Spoel <spoel at xray.bmc.uu.se>
>>Subject: Re: [gmx-users] gen_seed
>>To: Discussion list for GROMACS users
>><gmx-users at gromacs.org>
>>Message-ID: <1109166642.9838.1.camel at vangogh>
>>Content-Type: text/plain
>>
>>On Wed, 2005-02-23 at 14:26 +0100,
>>herbst at fhi-berlin.mpg.de wrote:
>>
>>>Hello all!
>>>
>>>I want to run two different simulations with the
>>
>>same system and have a
>>
>>>question concerning gen_seed.
>>>Is it ok when I use values like 7 and 13 for the
>>
>>two simulations, or are
>>
>>>these
>>>values too close together and I will get nearly
>>
>>identical velocity
>>
>>>distributions?
>>>How far apart should I chose the two gen_seeds?
>>
>>prime number are allways good. But it's ok if they
>>are different, unless
>>0, in which case it's generated
>>
>>>Thanks,
>>>Anna
>>>_______________________________________________
>>>gmx-users mailing list
>>>gmx-users at gromacs.org
>>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>>Please don't post (un)subscribe requests to the
>>
>>list. Use the 
>>
>>>www interface or send it to
>>
>>gmx-users-request at gromacs.org.
>>-- 
>>David.
>>
> 
> ________________________________________________________________________
> 
>>David van der Spoel, PhD, Assoc. Prof., Molecular
>>Biophysics group,
>>Dept. of Cell and Molecular Biology, Uppsala
>>University.
>>Husargatan 3, Box 596,          75124 Uppsala,
>>Sweden
>>phone:  46 18 471 4205          fax: 46 18 511 755
>>spoel at xray.bmc.uu.se    spoel at gromacs.org  
>>http://xray.bmc.uu.se/~spoel
>>
> 
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
>>
>>
>>
>>------------------------------
>>
>>Message: 3
>>Date: Wed, 23 Feb 2005 12:51:29 +0000 (GMT)
>>From: shailza singh <shailza_iitd at yahoo.com>
>>Subject: [gmx-users] total time for MDsimulation
>>To: gmx-users at gromacs.org
>>Message-ID:
>>
> 
> <20050223125129.74227.qmail at web8406.mail.in.yahoo.com>
> 
>>Content-Type: text/plain; charset=iso-8859-1
>>
>>Dear users,
>>i want to know that what is the total time taken for
>>simulation of a protein if a protein is run with
>>position restrained dynamics with 0.5 ns and without
>>position restrained for 1.0 ns? 
>>Is the total time accounted will be 1.0 ns only
>>taking
>>into account the full MD run or 1.5 ns taking into
>>account both short and full MD run?
>>
>>Also, I would like to clear about my doubt for full
>>MD
>>run?Should it be run for a longer period of time
>>than
>>short MD run or we can set the same number of steps
>>as
>>that of position restrained dynamics..only barring
>>define=-Dposres...
>>
>>Any help would be greatly appreciated.
>>Thanking you
>>shailza.
>>
>>
> 
> ________________________________________________________________________
> 
>>Yahoo! India Matrimony: Find your life partner
>>online
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>>
>>------------------------------
>>
>>Message: 4
>>Date: Wed, 23 Feb 2005 16:03:17 +0100
>>From: "Hendrik Preuss"
>><hendrik.preuss at chemie.uni-regensburg.de>
>>Subject: [gmx-users] g_cluster
>>To: <gmx-users at gromacs.org>
>>Message-ID:
>><s21ca950.053 at gw.ngate.uni-regensburg.de>
>>Content-Type: text/plain; charset=US-ASCII
>>
>>Dear gmx users,
>>
>>some things are puzzling me with g_cluster:
>>1. In June 2004 Roman Affentranger wrote about a bug
>>in g_cluster: The
>>cluster centers and the average RMSD values reported
>>in the log-file are
>>incorrectly determined. My question is: Can I use
>>g_cluster as it exists
>>or do I really have to change the source code to get
>>appropriate
>>clusters with average/center structures?
>>
>>2. Which cluster method would you recommend to gain
>>useful structures
>>of a 2.5ns MD of a GPCR in a bilayer environment
>>(full linkage, Jarvis
>>Patrick or gromos)?
>>
>>Thanks a lot for your help,
>>Hendrik
>>
>>
>>------------------------------
>>
>>Message: 5
>>Date: Wed, 23 Feb 2005 16:36:46 +0100
>>From: Maik Goette <mgoette at mpi-bpc.mpg.de>
>>Subject: Re: [gmx-users] total time for MDsimulation
>>To: Discussion list for GROMACS users
>><gmx-users at gromacs.org>
>>Message-ID: <421CA30E.30001 at mpi-bpc.mpg.de>
>>Content-Type: text/plain; charset=ISO-8859-1;
>>format=flowed
>>
>>
> 
> === message truncated ===
> 
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