[gmx-users] adding ETHANOL to CGennFF in gromacs has problem
Golshan Hejazi
golshan.hejazi at yahoo.com
Mon Sep 2 20:02:11 CEST 2013
Thanks Justin for looking at the files. I am using the gro and top file to generate a tpr with the following mdp file in order to see if everything is all right:
title = geometry-optimization
cpp = /usr/bin/cpp
include =
integrator = steep
comm_mode = Linear
dt = 0.001
nsteps = 1000000
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 1000
nstvout = 1000
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
xtc-precision = 100000
xtc_grps = System
energygrps = System
pbc = xyz
nstlist = 10
epsilon_r = 1.
ns_type = grid ; or grid I don't know
coulombtype = pme
vdwtype = Cut-off
fourierspacing = 0.12
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
epsilon_surface = 0
optimize_fft = yes
rlist = 0.8
rcoulomb = 0.8
rvdw = 0.8
emtol = 1.0
Yes, I am dealing with single molecule of ethanol. I can attach the tpr file and the resulting trr and gro file but it seems that the file size is big.
When I visualize the trajectory. in the second step, the molecule is already without any bond ... it is separated atoms. I don't think this is visualization problem since I already tried all trjconv -pbc option.
I am very confused.
Thank for helping
G.
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, September 2, 2013 1:34 PM
Subject: Re: [gmx-users] adding ETHANOL to CGennFF in gromacs has problem
Please make sure to keep the discussion on the mailing list.
On 9/2/13 1:27 PM, Golshan Hejazi wrote:
> This is the gro file that I am using:
> ETHANOL
> 9
> 1ETHA C1 1 3.133 3.266 0.008
> 1ETHA O1 2 3.244 3.350 -0.021
> 1ETHA HO1 3 3.324 3.296 -0.015
> 1ETHA H11 4 3.143 3.225 0.111
> 1ETHA H12 5 3.129 3.182 -0.065
> 1ETHA C2 6 3.007 3.351 -0.002
> 1ETHA H21 7 3.011 3.435 0.071
> 1ETHA H22 8 2.998 3.394 -0.104
> 1ETHA H23 9 2.917 3.290 0.019
> 3.41840 3.44350 3.38360
>
> This is what I added in the rtp:
>
> [ ETHA ]
> [ atoms ]
> C1 CG321 0.05 0
> O1 OG311 -0.65 1
> HO1 HGP1 0.42 2
> H11 HGA2 0.09 3
> H12 HGA2 0.09 4
> C2 CG331 -0.27 5
> H21 HGA3 0.09 6
> H22 HGA3 0.09 7
> H23 HGA3 0.09 8
> [ bonds ]
> C1 C2
> C1 O1
> C1 H11
> C1 H12
> O1 HO1
> C2 H21
> C2 H22
> C2 H23
>
> And this is the resulting topology:
>
> ; Include forcefield parameters
> #include "./charmm36.ff/forcefield.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> drug 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB
> chargeB massB
> ; residue 1 ETHA rtp ETHA q 0.0
> 1 CG321 1 ETHA C1 1 0.05 12.011 ; qtot 0.05
> 2 OG311 1 ETHA O1 2 -0.65 15.9994 ; qtot -0.6
> 3 HGP1 1 ETHA HO1 3 0.42 1.008 ; qtot -0.18
> 4 HGA2 1 ETHA H11 4 0.09 1.008 ; qtot -0.09
> 5 HGA2 1 ETHA H12 5 0.09 1.008 ; qtot 0
> 6 CG331 1 ETHA C2 6 -0.27 12.011 ; qtot -0.27
> 7 HGA3 1 ETHA H21 7 0.09 1.008 ; qtot -0.18
> 8 HGA3 1 ETHA H22 8 0.09 1.008 ; qtot -0.09
> 9 HGA3 1 ETHA H23 9 0.09 1.008 ; qtot 0
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1
> 1 4 1
> 1 5 1
> 1 6 1
> 2 3 1
> 6 7 1
> 6 8 1
> 6 9 1
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 2 7 1
> 2 8 1
> 2 9 1
> 3 4 1
> 3 5 1
> 3 6 1
> 4 7 1
> 4 8 1
> 4 9 1
> 5 7 1
> 5 8 1
> 5 9 1
> [ angles ]
> ; ai aj ak funct c0 c1 c2 c3
> 2 1 4 5
> 2 1 5 5
> 2 1 6 5
> 4 1 5 5
> 4 1 6 5
> 5 1 6 5
> 1 2 3 5
> 1 6 7 5
> 1 6 8 5
> 1 6 9 5
> 7 6 8 5
> 7 6 9 5
> 8 6 9 5
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2
> c3 c4 c5
> 4 1 2 3 9
> 5 1 2 3 9
> 6 1 2 3 9
> 2 1 6 7 9
> 2 1 6 8 9
> 2 1 6 9 9
> 4 1 6 7 9
> 4 1 6 8 9
> 4 1 6 9 9
> 5 1 6 7 9
> 5 1 6 8 9
> 5 1 6 9 9
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> [ system ]
> ; Name
> ETHANOL
>
> [ molecules ]
> ; Compound #mols
> drug 1
>
All of this looks perfectly normal. What are you trying to do when it flies
apart? Are you dealing with a single molecule only?
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users
mailing list