[gmx-users] Protein break after simulation

[ISHRAT JAHAN]

Here i am providing you the link of protein structure
https://we.tl/X4yEyZq2aR

On Sun, Sep 10, 2017 at 8:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
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