[gmx-users] adding a new atom type

[Shima Arasteh]

As I explained here before, I get an error ( some interactions seem to be assigned multiple times). I suspected the top file, so checked it  and visualized the output of em.mdp; the output seems to be correct and I don't see any bonds behaves strangely. 
As I studied in mailing lists it and you also mentioned , this may happen because of the insufficient minimization. I'm wondering how a good and sufficient minimization  is provided? 



Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Friday, July 27, 2012 10:51 PM
Subject: Re: [gmx-users] adding a new atom type



On 7/27/12 1:08 PM, Shima Arasteh wrote:
>
>
> Which parameter is supposed to be changed to get the sufficient minimized system? Would anyone guide me  please?
>

This question is very vague.  In principle, any system can be minimized but the 
definition of "sufficient" depends on your goals.

-Justin

> Thanks in advance
>
> Cheers,
> Shima
>
>
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc:
> Sent: Wednesday, July 25, 2012 4:37 PM
> Subject: Re: [gmx-users] adding a new atom type
>
>
>
> On 7/25/12 7:58 AM, Shima Arasteh wrote:
>>
>>
>>     Some time ago I defined a new residue and after running grompp I got an error as there are some interactions assigned multiple times. Then I decided to duplicate the atoms involved in that residue to avoid this error.
>
> That error usually indicates your system is crashing and the DD algorithm is failing.  That means either the coordinates are insufficiently minimized, the topology is incorrect, or the .mdp settings are leading to instability.
>
>> Next I renamed the atomtypes in atometypes.atp as below:
>>     ZC    12.01100 ;    carbonyl C, peptide backbone
>> ZCT1    12.01100 ;    aliphatic sp3 C for CH
>> ZCT3    12.01100 ;    aliphatic sp3 C for CH3
>> ZO    15.99900 ;    carbonyl oxygen
>> ZHC    1.00800 ;    N-ter H
>> ZNH1    14.00700 ;    peptide nitrogen
>> ZH    1.00800 ;    polar H
>> ZHB    1.00800 ;    backbone H
>> ZHA    1.00800 ;    nonpolar H
>>
>> Then I wanted to modify the .itp file, got in to the trouble; I couldn't find the C atomtype in nonbonded.itp file. Actually I don't know what to do now!
>>
>
> Start over with a fresh set of force field files that you haven't experimented with and troubleshoot the stability of your system.  If you Google or search the mailing list archive for this error, tons of useful results show up.
>
> -Justin
>
> -- ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> -- gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================