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.
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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
