[gmx-users] Re: change in the secondary structure after simulation
bharat gupta
bharat.85.monu at gmail.com
Thu Jan 27 14:25:34 CET 2011
> I didn't gave any -c flag while md run .. and there is no confout.gro in
> my folder .. I have attached the graph obtained after energy minimzation ..
> I want to ask why the graph is not coming like the one shown in the tutorial
> .. I guess I asked that same question earlier also ?? .. Here is the
> details of energy minimization result
>
> Steepest Descents converged to Fmax < 1000 in 720 steps
> Potential Energy = -6.7970475e+05
> Maximum force = 9.5201904e+02 on atom 78
> Norm of force = 1.9553707e+01
> On Thu, Jan 27, 2011 at 5:12 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> bharat gupta wrote:
>>
>>> I don't think that there is any problem in the structure .. since I am
>>> simulating the crystal structure taken from PDB ... and I have checked the
>>> structure generated after pdb2gmx and solvation..
>>> Since I am reapeating the simulation again I want to know and I am on
>>> energy minimzation step I want to know .. how can I retrieve the structure
>>> after minimization ..
>>>
>>>
>> The structure after minimization (or any process done by mdrun) is
>> contained in whatever filename you passed to the -c flag. If you haven't
>> specified any name, it is confout.gro.
>>
>> -Justin
>>
>> On Thu, Jan 27, 2011 at 4:16 AM, Mark Abraham <Mark.Abraham at anu.edu.au<mailto:
>>> Mark.Abraham at anu.edu.au>> wrote:
>>>
>>> On 27/01/2011 11:11 PM, bharat gupta wrote:
>>>
>>>> I used the same .mdp files that are given in the lysozyme tutorial
>>>> .. Since I was knowing what all parameters to change .. but after
>>>> energy minimization and equilibration steps , the graphs that I
>>>> got were fine ... even the rmsd graph of the final structure is
>>>> also fine .. I have attached the final rmsd graph of the structure ..
>>>>
>>>
>>> That suggests the problem was in the structure you started the
>>> simulation from, like I've suggested a few times now :-)
>>>
>>> Mark
>>>
>>>
>>>
>>>> On Thu, Jan 27, 2011 at 3:44 AM, Justin A. Lemkul <jalemkul at vt.edu
>>>> <mailto:jalemkul at vt.edu>> wrote:
>>>>
>>>>
>>>>
>>>> bharat gupta wrote:
>>>>
>>>> I generated the secondary structure profile of structure
>>>> retrieved from the last frame of the simulation ... In
>>>> that profile those amino acids that are shown as loops in
>>>> VMD doesnot have any secondary structure assignment ... it
>>>> means that during simulation the structure got changed
>>>> some how ... and It's really surprising ?? ... Can u tell
>>>> me where can the fault be as I am planning to do the
>>>> simulation again and this time I will check the structure
>>>> after every step .. but for that I want to know how can I
>>>> save the structure after every step say for eg. after
>>>> energy minimization ..
>>>>
>>>>
>>>> Secondary structure is dependent upon the chosen force field
>>>> and the .mdp settings. Since you've posted neither, there's
>>>> no way to tell what might be to blame.
>>>>
>>>> You can save more frequently by setting the proper output
>>>> controls. Read in the manual about the nst* options and set
>>>> the accordingly.
>>>>
>>>> -Justin
>>>>
>>>> On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul
>>>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>>>>
>>>>
>>>>
>>>> Mark Abraham wrote:
>>>>
>>>>
>>>>
>>>> On 01/27/11, *bharat gupta *
>>>> <bharat.85.monu at gmail.com <mailto:bharat.85.monu at gmail.com>
>>>> <mailto:bharat.85.monu at gmail.com
>>>> <mailto:bharat.85.monu at gmail.com>>> wrote:
>>>>
>>>> I actually don't understand exactly what u are
>>>> asking ..
>>>> since I am not an expert with gromacs..
>>>>
>>>>
>>>> Please leave the old context for the discussion in
>>>> future
>>>> emails. Only you are paying so much attention to
>>>> your work that
>>>> you can be sure of remembering things :-)
>>>>
>>>> If your simulation started with these strands
>>>> unfolded, then
>>>> your problem is somewhere else. However, you have
>>>> to be able to
>>>> tell us what was the initial conformation, and when
>>>> your "first
>>>> trajectory frame" (per last email) happened in the
>>>> simulation.
>>>>
>>>>
>>>> I would also add that VMD does a fairly poor job
>>>> sometimes of
>>>> guessing secondary structure. So if no beta strand was
>>>> present in
>>>> the very first frame, that doesn't necessarily mean the
>>>> secondary
>>>> structure wasn't stable, it just means VMD didn't
>>>> display it properly.
>>>>
>>>> -Justin
>>>>
>>>> Mark
>>>>
>>>>
>>>> I don't know when is was written .. Here are
>>>> some lines from
>>>> the log files of simulation ...
>>>> Statistics over 1500001 steps using 300001 frames
>>>>
>>>> Energies (kJ/mol)
>>>> Angle Proper Dih. Ryckaert-Bell.
>>>> LJ-14
>>>> Coulomb-14
>>>> 7.35090e+03 4.37413e+02 3.60104e+03
>>>> 5.26705e+03
>>>> 2.58894e+04
>>>> LJ (SR) Disper. corr. Coulomb (SR)
>>>> Coul. recip.
>>>> Potential
>>>> 1.05399e+05 -2.92853e+03 -6.79288e+05
>>>> -1.07015e+05
>>>> -6.41286e+05
>>>> Kinetic En. Total Energy Temperature
>>>> Pres. DC (bar)
>>>> Pressure (bar)
>>>> 1.03484e+05 -5.37802e+05 3.00003e+02
>>>> -2.37485e+02
>>>> 1.02890e+00
>>>> Constr. rmsd
>>>> 0.00000e+00
>>>>
>>>> Box-X Box-Y Box-Z
>>>> 7.42618e+00 7.42618e+00 7.42618e+00
>>>>
>>>> Total Virial (kJ/mol)
>>>> 3.44183e+04 3.40020e+01 -1.17357e+01
>>>> 3.42160e+01 3.45369e+04 -2.46337e+01
>>>> -1.16644e+01 -2.48479e+01 3.44949e+04
>>>>
>>>> Pressure (bar)
>>>> 1.99809e+00 9.48448e-02 4.57909e-01
>>>> 7.74354e-02 4.97824e-01 1.84797e+00
>>>> 4.52125e-01 1.86535e+00 5.90776e-01
>>>>
>>>> Total Dipole (D)
>>>> -1.86272e+02 4.46310e+01 2.08554e+02
>>>>
>>>> T-Protein T-non-Protein
>>>> 2.99904e+02 3.00013e+02
>>>>
>>>>
>>>> M E G A - F L O P S A C C O U N T I N G
>>>>
>>>>
>>>> There were in total 1502 frames (as shown in
>>>> VMD )...
>>>> I don't know about how it compared with the
>>>> coordinates of
>>>> the structure that I gave to grompp
>>>>
>>>> --------
>>>>
>>>> Pls guide
>>>>
>>>>
>>>>
>>>>
>>>> -- Bharat
>>>> Ph.D. Candidate
>>>> Room No. : 7202A, 2nd Floor
>>>> Biomolecular Engineering Laboratory
>>>> Division of Chemical Engineering and Polymer
>>>> Science
>>>> Pusan National University
>>>> Busan -609735
>>>> South Korea
>>>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>>> Mobile no. - 010-5818-3680
>>>> E-mail : monu46010 at yahoo.com
>>>> <mailto:monu46010 at yahoo.com> <mailto:monu46010 at yahoo.com
>>>> <mailto:monu46010 at yahoo.com>>
>>>> <mailto:monu46010 at yahoo.com
>>>> <mailto:monu46010 at yahoo.com> <mailto:monu46010 at yahoo.com
>>>> <mailto:monu46010 at yahoo.com>>>
>>>>
>>>>
>>>>
>>>> -- ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> MILES-IGERT Trainee
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu
>>>>
>>>> <http://vt.edu/>> | (540) 231-9080
>>>>
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
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>>>>
>>>>
>>>> -- Bharat
>>>> Ph.D. Candidate
>>>> Room No. : 7202A, 2nd Floor
>>>> Biomolecular Engineering Laboratory
>>>> Division of Chemical Engineering and Polymer Science
>>>> Pusan National University
>>>> Busan -609735
>>>> South Korea
>>>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>>> Mobile no. - 010-5818-3680
>>>> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>>>> <mailto:monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>>
>>>>
>>>>
>>>> -- ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> MILES-IGERT Trainee
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
>>>> -- gmx-users mailing list gmx-users at gromacs.org
>>>> <mailto:gmx-users at gromacs.org>
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>>>>
>>>>
>>>>
>>>>
>>>> -- Bharat
>>>> Ph.D. Candidate
>>>> Room No. : 7202A, 2nd Floor
>>>> Biomolecular Engineering Laboratory
>>>> Division of Chemical Engineering and Polymer Science
>>>> Pusan National University
>>>> Busan -609735
>>>> South Korea
>>>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>>> Mobile no. - 010-5818-3680
>>>> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>>>>
>>>>
>>>
>>> --
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>>>
>>>
>>> --
>>> Bharat
>>> Ph.D. Candidate
>>> Room No. : 7202A, 2nd Floor
>>> Biomolecular Engineering Laboratory
>>> Division of Chemical Engineering and Polymer Science
>>> Pusan National University
>>> Busan -609735
>>> South Korea
>>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>> Mobile no. - 010-5818-3680
>>> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>
>>>
>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> Please don't post (un)subscribe requests to the list. Use the www
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>>
>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com
>
>
--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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