[gmx-users] Protein break after simulation
Justin Lemkul
jalemkul at vt.edu
Mon Sep 11 13:56:47 CEST 2017
On 9/11/17 2:43 AM, ISHRAT JAHAN wrote:
> how can i check whether the structure is whole or not in .tpr file? After
> trjconv whole stage i got broken structure.
This is beyond just a "broken" structure. No amount of PBC manipulation
will fix this; it's as if the topology wasn't sound and you are missing
bonds or something. Did grompp issue any warnings? Did you override
anything with -maxwarn when running grompp?
-Justin
> On Sun, Sep 10, 2017 at 9:00 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> You seem to reporting that your system isn't whole. Is it whole after the
>> trjconv -whole stage? Is the structure in that .tpr whole?
>>
>> Mark
>>
>> On Sun, Sep 10, 2017 at 9:27 AM ISHRAT JAHAN <jishrat17 at gmail.com> 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.
>>> 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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