[gmx-users] Re: change in the secondary structure after simulation
Justin A. Lemkul
jalemkul at vt.edu
Thu Jan 27 14:12:08 CET 2011
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
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> <mailto:gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>>
>>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search
>> before posting!
>> Please don't post (un)subscribe requests to the list.
>> Use the www
>> interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>
>> <mailto:gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>>.
>>
>> Can't post? Read
>> http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>> --
>> 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>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>> --
>> 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>
>>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> --
> 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
========================================
More information about the gromacs.org_gmx-users
mailing list