On 9/10/17 3:27 AM, ISHRAT JAHAN wrote:
Dear Justin
I have used all the commands given in the link provided by you but unable
to get the solution.
commands used by me are-
trjconv -f prtn_full.xtc -s prtn_md.tpr -o prtn_md_whole.xtc -pbc whole -n
prtn_drg.ndx
trjconv -f prtn_md_whole.xtc -s prtn_md.tpr -o prtn_md_cluster.xtc -pbc
cluster -n prtn_drg.ndx
trjconv -f prtn_md_cluster.xtc -s prtn_md.tpr -o prtn_md_ref.gro -b 0 -e 0
-n prtn_drg.ndx
when i load the prtn_md_ref.gro in vmd i still get the unusual structure of
protein.
What does "unusual" mean? You're probably going to have to post some pictures
online and provide a URL.
-Justin
Please help me if i did not get the point and also check my full.mdp file
whether it is correct or not, given below-
;^M
title = Yo^M
cpp = /usr/bin/cpp^M
constraints = all-bonds^M
integrator = md^M
dt = 0.002 ; ps !^M
nsteps = 50000000 ; total 100000 ps.^M
nstcomm = 100^M
nstxout = 25000^M
nstvout = 500000^M
nstfout = 500000^M
nstlog = 500000^M
nstenergy = 50000^M
nstxtcout = 50000^M
xtc-precision = 10^M
nstlist = 10^M
ns_type = grid^M
rlist = 0.9^M
coulombtype = PME^M
rcoulomb = 1.2^M
rvdw = 1.2^M
fourierspacing = 0.12^M
fourier_nx = 0^M
fourier_ny = 0^M
fourier_nz = 0^M
pme_order = 4^M
ewald_rtol = 1e-5^M
optimize_fft = yes^M
; Berendsen temperature coupling is on in two groups^M
Tcoupl = V-rescale^M
tc-grps = Protein Non-Protein^M
tau_t = 0.1 0.1^M
ref_t = 310 310^M
; Energy monitoring^M
energygrps = Protein Non-Protein
; Isotropic pressure coupling is now on^M
Pcoupl = berendsen^M
Pcoupltype = isotropic^M
tau_p = 0.5^M
compressibility = 4.5e-5^M
5,1 40%
ref_p = 1.0^M
; Generate velocites is off at 310 K.^M
gen_vel = no^M
gen_temp = 310^M
gen_seed = 173529^M
^M
Thanks in advance
On Sat, Sep 9, 2017 at 7:04 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 9/9/17 1:50 AM, ISHRAT JAHAN wrote:
Dear all,
I have done 100ns md simulation of protein with drug using amber99sb.ff
with gromacs-5.1.4 version. After simulation i found my protein broken
into
smaller parts in .gro file but when i load the final xtc file to pr.gro
molecule does not break. I have applied -pbc nojump ,cluster and whole but
unable to solve the problem.
Will anyone help me to solve the above problem.
We'll need to see your commands, exactly as issued, to be able to say
anything. In general:
http://www.gromacs.org/Documentation/Terminology/Periodic_
Boundary_Conditions#Suggested_trjconv_workflow
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
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