[Fwd: Re: [gmx-users] coarse-grained model]
Yang Ye
leafyoung81-group at yahoo.com
Thu Jul 13 18:17:35 CEST 2006
Hi, Dongsheng
By checking mdlib/force.c, it is indeed that only one 1-4 table is read.
David, would you like to give some clue in adding support for multiple
1-4 tables?
Regards,
Yang Ye
-------- Original Message --------
Subject: Re: [gmx-users] coarse-grained model
Date: Thu, 13 Jul 2006 08:32:55 -0400
From: Dongsheng Zhang <dong at pampas.chem.purdue.edu>
To: Yang Ye <leafyoung81-group at yahoo.com>
Yang Ye,
Thank you for your help! I can use the table without any complaint, but it seems that gromacs can only read the first tablep**.xvg file
The following is from my log file:
Table routines are used for coulomb: FALSE
Table routines are used for vdw: TRUE
Cut-off's: NS: 1.4 Coulomb: 1.4 LJ: 1.4
System total charge: 0.000
Read user tables from table_EO_EO.xvg with 1251 data points.
Tabscale = 500 points/nm
Generated table with 1200 data points for COUL.
Tabscale = 500 points/nm
Read user tables from table_EO_PO.xvg with 1251 data points.
Tabscale = 500 points/nm
Generated table with 1200 data points for COUL.
Tabscale = 500 points/nm
Read user tables from table_PO_PO.xvg with 1251 data points.
Tabscale = 500 points/nm
Generated table with 1200 data points for COUL.
Tabscale = 500 points/nm
Read user tables from tablep_EO_EO.xvg with 1251 data points.
Tabscale = 500 points/nm
Generated table with 500 data points for 1-4 COUL.
I have also input tablep_PO_PO.xvg and tablep_EO_PO.xvg, but it seems
that gromacs can only recognize the first tablep***.xvg file, which is
tablep_EO_EO.xvg.
The following is from my mdp file:
energygrps = EO PO
energygrp_table = EO EO PO PO EO PO
coulombtype = Cut-off; PME;
vdw-type = user ;cut-off
The command I used is :
mpirun -np 2 mdrun_mpi -s full -o full -c full -g full -e full -x full
-v -table table.xvg -tablep tablep_EO_EO.xvg tablep_PO_PO.xvg
tablep_EO_PO.xvg >& full.job &
Could you please help me to find what's wrong?
All the best!
Dongsheng
On Wed, 2006-07-12 at 13:37 +0800, Yang Ye wrote:
> Dongsheng Zhang wrote:
> > Yang Ye,
> >
> > I am sorry to tell you I am not clear yet. Do you think I need to
> > specify energygrps and corresponding energygrp_table?
> >
> > If so, then I got any error message. gp1 includes atom A, and gp3
> > includes atom A and B. Gromacs will complain that atoma has been in two
> > groups. Each group uses it own different table, but the group members
> > are overlapping bwteen some groups. How can I fix it?
> >
> You don't need to define 1-4 group again. with -table and -tablep for
> mdrun, between energy group A and B, 1-2 interaction will be looked up
> from table_A_B.xvg and 1-4 interaction will be looked up from
> tablep_A_B.xvg.
>
> And also, energygrps shall corresponds to energygrp_table.
>
> So, instead to have
>
> energygrps = gp1 gp2 gp3 gp4 gp5 gp6 ... gp12
> energygrp_table = A A B B C C A B A C B C A14 A14 B14 B14 C14 C14 A14
> B14 A14 C14 B14 C14
>
> You shall have
>
> energygrps = A B C ...
> energygrp_table = A A B B C C A B A C B C
>
> > If not, I really have concern how gromacs knows to look for
> > table_A_A.xvg when it calculates A-A nonbonded interaction and look for
> > table_A14_A14.xvg when it calculates 1-4 interaction between A and A
> > monomers.
> >
> > Could you please give me more instruction? Thank you for your help!
> >
> >
> > Dongsheng
> >
> >
> > On Wed, 2006-07-12 at 11:18 +0800, Yang Ye wrote:
> >
> >> Don't worry about that.
> >> mdrun -tablep {tablep} will follow the scheme {tablep}_A_A.xvg,
> >> {tablep}_B_B.xvg ...
> >> {tablep} may be replaced by your own filename.
> >>
> >> Yang Ye
> >>
> >> Dongsheng Zhang wrote:
> >>
> >>> Yang ye,
> >>>
> >>> Thank you very much.
> >>>
> >>> I have three different monomers in my system, so I have 6 different
> >>> regular VMDs and 6 different 1-4 interactions. Could you please tell me
> >>> how to organize those table.xvg files?
> >>>
> >>> energygrps = gp1 gp2 gp3 gp4 gp5 gp6 ... gp12
> >>> energygrp_table = A A B B C C A B A C B C A14 A14 B14 B14 C14 C14 A14
> >>> B14 A14 C14 B14 C14
> >>>
> >>> If I set as the above, I wonder how gromacs know the last 6 table is for
> >>> 1-4 interaction.
> >>>
> >>> All the best!
> >>>
> >>> Dongsheng
> >>>
> >>> On Wed, 2006-07-12 at 09:54 +0800, Yang Ye wrote:
> >>>
> >>>
> >>>> mdrun -tablep
> >>>>
> >>>> Dongsheng Zhang wrote:
> >>>>
> >>>>
> >>>>> Hello, GMX users,
> >>>>>
> >>>>> I have a coarse-grained model. Both 1-4 and regular vdw interaction are
> >>>>> tabulated, but no electrostatic interaction. Since there is no entry for
> >>>>> 1-4 interaction in energy_table. I am thinking to fool gromacs by
> >>>>> treating 1-4 interactions as electrostatic interactions, in other words,
> >>>>> every time when 1-4 interaction energy needed, I will ask gromacs to
> >>>>> calculate COUL energy by reading energy_table. Does anyone know where
> >>>>> 1-4 interaction is calculated and how I can switch it to calculate COUL
> >>>>> energy in the source code? Any help will be highly appreciated!
> >>>>>
> >>>>>
> >>>>> All the best!
> >>>>>
> >>>>>
> >>>>> Dongsheng
> >>>>> _______________________________________________
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