[gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093)

[swati rana]

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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