[gmx-users] Re: gmx-users Digest, Vol 62, Issue 68

Gerrit Groenhof ggroenh at gwdg.de
Sun Jun 14 21:46:25 CEST 2009 

>


What do you mean by full QM system? A molecule without environment can  
be simulated at the QM only level.

Use oniom with one layer, which is then the full system.

Gerrit


> -1
>
> hi all,
>
> i am interested in doing full ab initio molecular dynamics using
> gromacs, coupled to either GAMESS or Gaussian. i am not interested in
> using any single or multilayer QM/MM scheme. it doesn't appear that
> gromacs supports a full QM system. does anyone know the origin of this
> limitation? or, perhaps any easy ways/tricks around it?
>
> traditionally i would do this with other software, though i am
> interested specifically in doing parallel tempering work at the ab
> initio level, and gromacs is a good fit.
>
> secondly, information on coupling gromacs to GAMESS or Gaussian is
> sparse. any links to known documentation would be welcome!
>
> thanks in advance,
> anthony
>
> -- 
> Anthony B. Costa
> Purdue University
> Department of Chemistry
> 560 Oval Drive, #365
> West Lafayette, IN 47907
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 13 Jun 2009 10:39:44 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Question about applying a restriction on the
> 	movement	of a molecule in z direction....
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A32F550.8070804 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Alberto Sergio Garay wrote:
>> Hi all
>>
>> I need to avoid that a solute molecule cross to the other side of my
>> lipid bilayer.and I have thought in several alternatives, which I'm  
>> not
>> sure whether they are posible in gromacs so I decided to ask for
>> suggestions.
>
> In a periodic system with one symmetric bilayer and one block of
> solvent, there seems to be little value in such a restriction.
>
>> Could anyone give any possible alternative to restrict the movement  
>> of
>> my molecule in the z direction only when it reaches a certain z  
>> distance
>> from, for example the center of the bilayer ?
>
> Pick a few key atoms in the bilayer, decide how far you want to let it
> roam from the bilayer, do your Pythagoras and work out the maximum
> displacement from a key atom that is consistent with your maximum
> bilayer displacement, invoke a fudge factor, and use distance  
> restraints
> on those key atoms.
>
> Mark
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 13 Jun 2009 10:44:43 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] ab initio parallel tempering
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A32F67B.6070503 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Anthony Costa wrote:
>> hi all,
>>
>> i am interested in doing full ab initio molecular dynamics using
>> gromacs, coupled to either GAMESS or Gaussian. i am not interested in
>> using any single or multilayer QM/MM scheme. it doesn't appear that
>> gromacs supports a full QM system. does anyone know the origin of  
>> this
>> limitation? or, perhaps any easy ways/tricks around it?
>>
>> traditionally i would do this with other software, though i am
>> interested specifically in doing parallel tempering work at the ab
>> initio level, and gromacs is a good fit.
>>
>> secondly, information on coupling gromacs to GAMESS or Gaussian is
>> sparse. any links to known documentation would be welcome!
>
> I can only suggest starting here http://oldwiki.gromacs.org/index.php/QMMM
>
> Mark
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 13 Jun 2009 12:00:11 +0530 (IST)
> From: "Ms. Aswathy S" <aswathys at amritapuri.amrita.edu>
> Subject: [gmx-users] Error in hdb file ffG43a1.hdb
> To: gmx-users <gmx-users at gromacs.org>
> Message-ID:
> 	<29124151.2252521244874611261.JavaMail.root at durga.amrita.ac.in>
> Content-Type: text/plain; charset=utf-8
>
> Hi,
>
> I have upgraded my gromacs version to 3.3.3 from 3.2.1. When I tried  
> to run the pdb2gmx i got the follo: error. From the previous post I  
> guess that i should edit this ffG43a1.hdb. but my input is a protein  
> file so ..so is this necessary or any other way to rectify this  
> problem???
>
> -------------------------------------------------------
> Program pdb2gmx_mpi, VERSION 3.3.3
> Source code file: h_db.c, line: 95
>
> Fatal error:
> Error in hdb file ffG43a1.hdb:
> Wrong number of control atoms (2 iso 3) on line:
>       1       1       N       -C      CA
>
> Thanks in advance,
> Aswathy
> Dept. Biotechnology
> Ext. 3108
>
>
> ------------------------------
>
> Message: 5
> Date: Sat, 13 Jun 2009 14:39:33 +0530 (IST)
> From: "Ms. Aswathy S" <aswathys at amritapuri.amrita.edu>
> Subject: Re: [gmx-users] Error in hdb file ffG43a1.hdb
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> 	<9429901.2257241244884173226.JavaMail.root at durga.amrita.ac.in>
> Content-Type: text/plain; charset=utf-8
>
> Please ignore this post. I rectified the problem by using the GMXLIB  
> export.
>
> Thank you very much for all the support
>
> Aswathy
>
> Dept. Biotechnology
> Ext. 3108
>
> ----- Original Message -----
> From: "Ms. Aswathy S" <aswathys at amritapuri.amrita.edu>
> To: "gmx-users" <gmx-users at gromacs.org>
> Sent: Saturday, June 13, 2009 12:00:11 PM GMT +05:30 Chennai,  
> Kolkata, Mumbai, New Delhi
> Subject: [gmx-users] Error in hdb file ffG43a1.hdb
>
> Hi,
>
> I have upgraded my gromacs version to 3.3.3 from 3.2.1. When I tried  
> to run the pdb2gmx i got the follo: error. From the previous post I  
> guess that i should edit this ffG43a1.hdb. but my input is a protein  
> file so ..so is this necessary or any other way to rectify this  
> problem???
>
> -------------------------------------------------------
> Program pdb2gmx_mpi, VERSION 3.3.3
> Source code file: h_db.c, line: 95
>
> Fatal error:
> Error in hdb file ffG43a1.hdb:
> Wrong number of control atoms (2 iso 3) on line:
>       1       1       N       -C      CA
>
> Thanks in advance,
> Aswathy
> Dept. Biotechnology
> Ext. 3108
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>
> ------------------------------
>
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>
> End of gmx-users Digest, Vol 62, Issue 68
> *****************************************

--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/

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