[gmx-users] Protein break after simulation

ISHRAT JAHAN jishrat17 at gmail.com
Mon Sep 11 15:50:10 CEST 2017 

no grompp not gives any warning neither i have used -maxwarn option.

On Mon, Sep 11, 2017 at 5:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>>>> <https://maps.google.com/?q=mands,+exactly+as+issued,+to+be+able+to&entry=gmail&source=g>
>>>>> 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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