[gmx-users] Re: change in the secondary structure after simulation
Thomas Piggot
t.piggot at soton.ac.uk
Thu Jan 27 14:31:02 CET 2011
Hi Bharat,
If you have used the -deffnm option then the output gro will be called
whatever name you used for the -deffnm option and not the default
confout.gro.
Tom
Justin A. Lemkul wrote:
>
> bharat gupta wrote:
>> 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've never heard of such a thing. mdrun produces several files automatically:
> traj.trr, ener.edr, md.log, and confout.gro. The output configuration is always
> written. If it wasn't, then something is preventing mdrun from writing this
> file (full disk, read/write permissions, etc).
>
>> .. 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
>>
>
> The shape of the graph is nearly identical. You converged to an acceptable
> energy and force, so what's the problem?
>
> If you're following the tutorial's procedure with a different system, there is
> absolutely no reason to expect that one system will converge to the same
> potential energy as another. They're fundamentally different. Even if you are
> working with the same system, there can be differences in the final energy. EM
> is just a procedure to optimize the orientation of the molecules in the system.
> It may converge somewhat differently each time you do it.
>
> -Justin
>
>> 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
>> <mailto: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>
>> <mailto: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>
>> <mailto: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>>
>> <mailto: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>>
>> <mailto: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>>>
>> <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
>> <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 <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
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>> <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/>
>> | (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>>
>>
>>
>>
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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
>>
>> ========================================
>> --
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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
>
> ========================================
> --
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--
Dr Thomas Piggot
University of Southampton, UK.
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