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