[gmx-users] Re: Reg: Gromacs binary liquid-liquid simulation
Justin A. Lemkul
jalemkul at vt.edu
Mon Sep 13 14:24:48 CEST 2010
vinothkumar mohanakrishnan wrote:
> 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
>
You're trying to use an all-atom coordinate file with a united-atom force field.
Do not try to add atoms to the topology. Use an appropriate coordinate file.
Also, the charges assigned to the hexane molecule (like much of the output from
PRODRG) are probably not correct. In UA force fields like Gromos, aliphatic
groups should be uncharged. Note that there is a charge imbalance in your
molecule, such that there is a permanent, albeit small, net dipole on the
molecule. Ask yourself: does this model reflect reality?
> 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.
>
Perhaps the box you're using simply can't fit more than 101 molecules.
-Justin
> 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
> <mailto: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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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--
========================================
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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