[gmx-users] Re: Reg: Gromacs binary liquid-liquid simulation
vinothkumar mohanakrishnan
kmvinoth at gmail.com
Mon Sep 13 14:19:08 CEST 2010
hi i have 20 coordinates in the .gro file from PRODRG server where as i have
only 6 atom coordidates in the .top file this file also i got from PRODRG.
below i am giving both my .top file as well as .gro file for hexane. do i
manually edit the .top file from PRODRG to match the coordinates, if so
how?.my worry again is when i give this command
genbox -cp hexane_box.gro -ci hexane_box.gro -p hexane.top -o
hexane_multi.gro -nmol 100 -seed 1997
the .top file doesn't get updated with more number (say 101) of hexane
molecules in the molecules section.kindly advice me on this point.
hexane.top
#include "ffG43a1.itp"
[ moleculetype ]
; Name nrexcl
hexane 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 DRG CAA 1 -0.018 15.0350
2 CH2 1 DRG CAB 1 0.011 14.0270
3 CH2 1 DRG CAC 1 0.008 14.0270
4 CH2 1 DRG CAD 1 0.009 14.0270
5 CH2 1 DRG CAE 1 0.009 14.0270
6 CH3 1 DRG CAF 1 -0.019 15.0350
[ bonds ]
; ai aj fu c0, c1, ...
2 1 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAA
2 3 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAC
3 4 2 0.153 7150000.0 0.153 7150000.0 ; CAC CAD
4 5 2 0.153 7150000.0 0.153 7150000.0 ; CAD CAE
5 6 2 0.153 7150000.0 0.153 7150000.0 ; CAE CAF
[ pairs ]
; ai aj fu c0, c1, ...
1 4 1 ; CAA CAD
2 5 1 ; CAB CAE
3 6 1 ; CAC CAF
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 109.5 520.0 109.5 520.0 ; CAA CAB
CAC
2 3 4 2 109.5 520.0 109.5 520.0 ; CAB CAC
CAD
3 4 5 2 109.5 520.0 109.5 520.0 ; CAC CAD
CAE
4 5 6 2 109.5 520.0 109.5 520.0 ; CAD CAE
CAF
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih CAD CAC
CAB CAA
5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih CAE CAD
CAC CAB
6 5 4 3 1 0.0 5.9 3 0.0 5.9 3 ; dih CAF CAE
CAD CAC
; Include SPC water topology
#include "spc.itp"
[ system ]
hexane in water
[ molecules ]
;molecule name number
hexane 101
SOL 1764
hexane.gro
PRODRG COORDS
20
1DRG CAA 1 0.684 -0.063 1.332
1DRG HAA 2 0.684 0.013 1.254
1DRG HAB 3 0.583 -0.075 1.371
1DRG HAC 4 0.724 -0.158 1.295
1DRG CAB 5 0.778 -0.021 1.445
1DRG HAD 6 0.776 -0.098 1.522
1DRG HAE 7 0.744 0.077 1.479
1DRG CAC 8 0.923 -0.003 1.396
1DRG HAF 9 0.950 -0.087 1.332
1DRG HAG 10 0.985 0.007 1.485
1DRG CAD 11 0.940 0.127 1.316
1DRG HAH 12 0.913 0.211 1.380
1DRG HAI 13 0.878 0.117 1.227
1DRG CAE 14 1.085 0.145 1.267
1DRG HAJ 15 1.087 0.222 1.190
1DRG HAK 16 1.118 0.047 1.232
1DRG CAF 17 1.179 0.186 1.380
1DRG HAM 18 1.149 0.284 1.418
1DRG HAN 19 1.281 0.191 1.342
1DRG HAL 20 1.168 0.108 1.456
0.84818 0.84818 0.84818
Regards
Vinoth
On Mon, Sep 13, 2010 at 4:26 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> vinothkumar mohanakrishnan wrote:
>
>> i want to do MD for hexane-water system. I got hexane.gro and hexane..itp
>> from PRODRG 2.5 Beta server with that i made the hexane.top file. below is
>> the serious of commands i executed in gromacs, i am adding 200 hexane
>> molecules an 1115 water molecules. after the first genbox i checked my
>> topolgy file wheather the no .of hexane molecules got updated r increased to
>> 200 but it doesn't and remains as 1 and then i maually changed it to 200 in
>> the molecules section. i dont know where
>>
>
> Per your genbox command below, if you have one hexane (in hexane_box.gro)
> and you add 200 (with -nmol), you should then have 201 hexane molecules in
> the system.
>
>
> iam going wrong and i always get the error message as " number of
>> coordinates in coordinate file (hexane_solv.gro, 7365) does not match
>> topology (hexane.top, 4545) " while running grompp for energy minimisation.
>> i read the error gromacs (website) documentation and found that the
>> hexane.top r hexane.gro file is not getting updated, but iam helpless. any
>> help is highly appreciated. below is my topology file as well.
>>
>>
> Follow my previous advice and see if you can trace back where the error
> came from. Count the molecules in your .gro file, i.e.:
>
> grep OW hexane_solv.gro | wc -l
>
> will give you the number of water molecules. Do something analogous for
> hexane. You're off by 2820 atoms, which is in the ballpark of 940 waters,
> so something has broken down pretty badly somewhere.
>
> -Justin
>
>
> ; The force field files to be included
>> #include "ffG43a1.itp"
>>
>> ; Include hexane topology
>> #include "hexane.itp"
>>
>> ; Include SPC water topology
>> #include "spc.itp"
>>
>> [ system ]
>> hexane in Water
>>
>> [ molecules ]
>> ;molecule name number
>> hexane 200
>> SOL 1115
>> *
>> Commands*
>>
>> editconf -f hexane.gro -o hexane_box.gro -c -bt triclinic -box 8.31 3.01
>> 3.01
>>
>> genbox -cp hexane_box.gro -ci hexane_box.gro -p hexane.top -o
>> hexane_multi.gro -nmol 200 -seed 1997
>>
>> genbox -cp hexane_multi.gro -cs spc216.gro -p hexane.top -o
>> hexane_solv.gro
>>
>> grompp -f em.mdp -c hexane_solv.gro -p hexane.top -o hexane_em.tpr
>>
>> Regards
>> Vinoth
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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