On 10/28/13 3:30 AM, Santu Biswas wrote:
"Not working" is too vague a symptom for anyone to guess what the
problem
is, sorry.
Mark
On Oct 24, 2013 9:39 AM, "Santu Biswas" <santu.biswa...@gmail.com>
wrote:
dear users,
I am performing 500ps mdrun in vacuum for
polypeptide(formed
by 10-residues leucine) using gromacs_4.5.5(double-
precision) using
opls-aa/L force field.Input file for 500ps mdrun is given below
title = peptide in vaccum
cpp = /lib/cpp
; RUN CONTROL
integrator = md
comm_mode = ANGULAR
nsteps = 500000
dt = 0.001
; NEIGHBOR SEARCHING
nstlist = 0
ns_type = simple
pbc = no
rlist = 0
; OUTPUT CONTROL
nstxout = 1000
nstvout = 1000
nstxtcout = 0
nstlog = 1000
constraints = none
nstenergy = 1000
; OPTION FOR ELECTROSTATIC AND VDW
rcoulomb = 0
; Method for doing Van der Waals
rvdw = 0
; OPTIONS FOR WEAK COUPLING ALGORITHMS
tcoupl = V-rescale
tc_grps = Protein
tau_t = 0.1
ref_t = 300
gen_vel = yes
gen_temp = 300
Using the 500ps trajectory if i run g_hbond_d for calculating the
number
of
hydrogen bonds as a function of time using index file(where atom O and
atom
N H is used) it is not working.
Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is
also
not working.
I do not know why this is happening.
------
santu
--
Thanks Mark for your reply.
Using the 500ps trajectory i want to calculate the number of hydrogen
bonds as a function of time in vacuum .For this calculation i
have uesd
g_hbond_d -f traj_0-500ps.trr -s 500ps.tpr -n index.ndx -num
hbond-num.xvg -dist dist.xvg -ang angle.xvg
With what groups? Can there be any hydrogen bonds between those groups?
Is there a bug fixed in a version of g_hbond that isn't 2 years old? Did a
shorter trajectory work because it took less time? Does doing only one of
three analyses help things to work? You'd be much closer to a solution if
you'd tried some simplifications and done some detective work already ;-)
Programm was running .After 1 hour it was still running but there was no
output.
If I calculate the number of hydrogen bonds as a function of time in
water (no vacuum) using the same command line then there was no problem.
Same problem when I used g_rdf in vacuum.The commad line I have used
g_rdf_4.5.5 -f traj.trr -s 500ps.tpr -n index.ndx -o rdf.xvg and also
checked with -nopbc with the same command line.
RDF of what, in vacuum? What groups did you use?
The programm is running but in the output file nothing is written.
If I used g_rdf in water using the same command line there was no
problem.
OK - but does your analysis make sense in vacuum?
Mark
Thanks Mark for your reply
In the index file I mentioned C=O oxygen atom and N-H hydrogen atom. Now I
want to calculate the distance between O atom and N-H hydrogen atom using
g_rdf in vacuum.
Similarly using the same index file I want to calculate the number of
hydrogen bonds as a function of time in vacuum using g_hbond.
Yes there is a H bond between C=O oxygen atom of i-th residue and N-H
hydrogen of i+4-th residue.
I also checked with shorter trajectory there is also same problem .
Please let me know If there are any mistakes.
Does your system have a non-zero size? That is, are all the box vectors a
somewhat reasonable value? They are, of course, irrelevant for the simulation
(assuming pbc = no for in vacuo), but for analysis, you need a sensible box. If
you don't, you can recenter the trajectory using trjconv -box -center.
-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
==================================================
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