[gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093)
Emanuel Birru
Emanuel.Birru at monash.edu
Thu Mar 21 06:48:49 CET 2013
If the atom names in your gro file and in the top file are the same then I suggest to check how the sequence of the atoms looks like in your gro file. Is it POPC at the top and the water at the bottom as your topology suggested? If not swap them in the molecule section.
[ molecules ]
; molecule name nr.
POPC 128 ???
SOL 2460 ???
Cheers,
EB
-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of swati rana
Sent: Thursday, 21 March 2013 4:37 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093)
Dear Justin,
I am facing another problem i.e. IN removing the periodicity of the downloaded popc128a.pdb file.
Warning: atom name 6673 in topol_popc.top and popc128a.gro does not match
(HW1 - HW2)
Warning: atom name 6674 in topol_popc.top and popc128a.gro does not match
(HW2 - HW3)
Warning: atom name 6675 in topol_popc.top and popc128a.gro does not match (OW - OW1)
Warning: atom name 6676 in topol_popc.top and popc128a.gro does not match
(HW1 - HW2)
(more than 20 non-matching atom names)
WARNING 1 [file topol_popc.top, line 31]:
7380 non-matching atom names
atom names from topol_popc.top will be used
atom names from popc128a.gro will be ignored
This question has been asked by another person as well and in case the solution he suggested worked. But in my case everything in the pdb file is okie though i am getting this error. Please suggest what should be done.
spc.itp file is like this:
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
#ifndef HEAVY_H
1 OW 1 SOL OW 1 -0.82 15.99940
2 H 1 SOL HW1 1 0.41 1.00800
3 H 1 SOL HW2 1 0.41 1.00800
#else
1 OW 1 SOL OW 1 -0.82 9.95140
2 H 1 SOL HW1 1 0.41 4.03200
3 H 1 SOL HW2 1 0.41 4.03200
#endif
#ifndef FLEXIBLE
[ settles ]
; OW funct doh dhh
1 1 0.1 0.16330
[ exclusions ]
1 2 3
2 1 3
3 1 2
#else
[ bonds ]
; i j funct length force.c.
1 2 1 0.1 345000 0.1 345000
1 3 1 0.1 345000 0.1 345000
[ angles ]
; i j k funct angle force.c.
2 1 3 1 109.47 383 109.47 383
#endif
And topol file is:
;
; File 'topol_popc.top' was generated
; By user: swati (1000)
; On host: laptop
; At date: Wed Feb 27 14:16:52 2013
;
; This is your topology file
;
; Include chain topologies
#include "gromos43a1_lipid.ff/forcefield.itp"
; Include ligand toplogy
#include "gromos43a1_lipid.ff/ligand.itp"
; Include lipid topology
#include "popc.itp"
; Include water topology
#include "gromos43a1_lipid.ff/spc.itp"
; Include ion topologies
#include "gromos43a1_lipid.ff/ions.itp"
; System specifications
[ system ]
128-Lipid POPC Bilayer
[ molecules ]
; molecule name nr.
POPC 128
SOL 2460
Thanks in advance.
With Regards,
Swati.
On Mon, Mar 4, 2013 at 12:45 PM, swati rana <swati.rana088 at gmail.com> wrote:
> Dear Justin,
>
> Thanks a lot, your suggestions helped me a lot.
>
> With Regards,
> Swati
>
>
> On Sun, Mar 3, 2013 at 1:22 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 3/2/13 1:42 AM, swati rana wrote:
>>
>>> Hi Justin,
>>>
>>> Thanks a lot, that suggestion of yours helped. I am on the
>>> equilibration step and its running but nothing is happening on the
>>> terminal its just stagnant. Is it fine because its more than 17 hrs
>>> now. Is there some problem.
>>> After running the second command nothing is happening on the terminal.
>>>
>>> grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
>>>
>>> mdrun -deffnm nvt
>>>
>>> I am sorry as it is not a reasonable question to ask but i am just
>>> asking out of curiosity and lack of time.
>>>
>>>
>> If you're trying to run an MD simulation in serial, you'll get
>> terrible performance unless the system is very small (a few hundred
>> atoms). Most MD is conducted in parallel on high-performance
>> computing clusters, or at the very least on a multi-core workstation, again using parallelization.
>>
>> You won't get constant output in either case, since I/O is buffered
>> and write intervals depend on what you specify in the .mdp file. In
>> any case, if you're getting poor performance, you're probably simply
>> asking your computer to do something it's incapable of handling efficiently.
>>
>>
>> -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<http://www
>> .bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
>> --
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