On 28/07/2012 4:34 AM, Shima Arasteh wrote:
As I explained here before, I get an error ( some interactions seem to be
assigned multiple times).
And it's been suggested several times that your system may be
http://www.gromacs.org/Documentation/Terminology/Blowing_Up, and
diagnostic and management strategies are described there. Since you
haven't said whether it was immediately upon simulation start (so that
the topology might be doubtful, and probably only if you are the first
to find some new bug) or later on (when the topology is not directly to
blame for blowing up). Messing around duplicating atom types to try to
avoid the situation is presupposing the form of the solution to a
problem that you have not yet identified.
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.
OK, but the "bonds" you see there do not relate to the ones in your
topology.
http://www.gromacs.org/About_Gromacs/Related_Software/Visualization_Software.
So all you've seen is that nothing's gone wrong enough so far.
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?
Often whatever comes out of a single-precision EM run is fine. You have
not presented evidence that your minimization is insufficient, and there
are many other possible causes for blowing up. In the absence of a
description of your system, your .mdp file and how you've modified your
forcefield and/or topology, it's impossible to get effective help.
Mark
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul <jalem...@vt.edu>
To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@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 <jalem...@vt.edu>
To: Discussion list for GROMACS users <gmx-users@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
========================================
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