[gmx-users] Protein break after simulation

[ISHRAT JAHAN]

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 <jalemkul at 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
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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