[gmx-users] Protein break after simulation

[Justin Lemkul]

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 <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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-- 
==================================================

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

==================================================