On 9/2/13 2:02 PM, Golshan Hejazi wrote:
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
Note that your cutoffs are incorrect for strict adherence to CHARMM settings.
See extensive threads from recent days and weeks on this topic.
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.
The mailing list does not accept attachments, nor are those files particularly
informative (maybe the .gro, but that can easily just be pasted in an email for
a single-molecule system). Screenshots linked from some publicly accessible
image-sharing site work well.
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.
Measurements of intramolecular distances are more informative than whether or
not visualization software thinks there's actually a bond there. The topology
is definitive, visualization is not. There may certainly be a problem, but be
sure you're using quantitative assessments, not qualitative (and error-prone).
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
