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<div>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<br>
<br>Steepest Descents converged to Fmax < 1000 in 720 steps<br>Potential Energy = -6.7970475e+05<br>Maximum force = 9.5201904e+02 on atom 78<br>Norm of force = 1.9553707e+01 </div>
<div class="gmail_quote">On Thu, Jan 27, 2011 at 5:12 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
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<div><br><br>bharat gupta wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">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..<br>
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 ..<br><br></blockquote><br></div>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.<br>
<br>-Justin<br><br>
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<div>On Thu, Jan 27, 2011 at 4:16 AM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br> On 27/01/2011 11:11 PM, bharat gupta wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"> I used the same .mdp files that are given in the lysozyme tutorial<br> .. Since I was knowing what all parameters to change .. but after<br>
energy minimization and equilibration steps , the graphs that I<br> got were fine ... even the rmsd graph of the final structure is<br> also fine .. I have attached the final rmsd graph of the structure ..<br></blockquote>
<br> That suggests the problem was in the structure you started the<br> simulation from, like I've suggested a few times now :-)<br><br> Mark<br><br> <br></div>
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<div> On Thu, Jan 27, 2011 at 3:44 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div>
<div> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br><br><br><br> bharat gupta wrote:<br><br> I generated the secondary structure profile of structure<br>
retrieved from the last frame of the simulation ... In<br> that profile those amino acids that are shown as loops in<br> VMD doesnot have any secondary structure assignment ... it<br> means that during simulation the structure got changed<br>
some how ... and It's really surprising ?? ... Can u tell<br> me where can the fault be as I am planning to do the<br> simulation again and this time I will check the structure<br> after every step .. but for that I want to know how can I<br>
save the structure after every step say for eg. after<br> energy minimization ..<br><br><br> Secondary structure is dependent upon the chosen force field<br> and the .mdp settings. Since you've posted neither, there's<br>
no way to tell what might be to blame.<br><br> You can save more frequently by setting the proper output<br> controls. Read in the manual about the nst* options and set<br> the accordingly.<br><br>
-Justin<br><br> On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul<br> <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
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<div> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br><br><br><br> Mark Abraham wrote:<br>
<br><br><br> On 01/27/11, *bharat gupta *<br> <<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a> <mailto:<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>><br>
<mailto:<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a><br> <mailto:<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>>>> wrote:<br>
<br> I actually don't understand exactly what u are<br> asking ..<br> since I am not an expert with gromacs..<br><br><br> Please leave the old context for the discussion in<br>
future<br> emails. Only you are paying so much attention to<br> your work that<br> you can be sure of remembering things :-)<br><br> If your simulation started with these strands<br>
unfolded, then<br> your problem is somewhere else. However, you have<br> to be able to<br> tell us what was the initial conformation, and when<br> your "first<br>
trajectory frame" (per last email) happened in the<br> simulation.<br><br><br> I would also add that VMD does a fairly poor job<br> sometimes of<br> guessing secondary structure. So if no beta strand was<br>
present in<br> the very first frame, that doesn't necessarily mean the<br> secondary<br> structure wasn't stable, it just means VMD didn't<br> display it properly.<br>
<br> -Justin<br><br> Mark<br><br><br> I don't know when is was written .. Here are<br> some lines from<br> the log files of simulation ...<br>
Statistics over 1500001 steps using 300001 frames<br><br> Energies (kJ/mol)<br> Angle Proper Dih. Ryckaert-Bell. LJ-14<br> Coulomb-14<br>
7.35090e+03 4.37413e+02 3.60104e+03 5.26705e+03<br> 2.58894e+04<br> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.<br>
Potential<br> 1.05399e+05 -2.92853e+03 -6.79288e+05 -1.07015e+05<br> -6.41286e+05<br> Kinetic En. Total Energy Temperature<br>
Pres. DC (bar)<br> Pressure (bar)<br> 1.03484e+05 -5.37802e+05 3.00003e+02 -2.37485e+02<br> 1.02890e+00<br> Constr. rmsd<br>
0.00000e+00<br><br> Box-X Box-Y Box-Z<br> 7.42618e+00 7.42618e+00 7.42618e+00<br><br> Total Virial (kJ/mol)<br>
3.44183e+04 3.40020e+01 -1.17357e+01<br> 3.42160e+01 3.45369e+04 -2.46337e+01<br> -1.16644e+01 -2.48479e+01 3.44949e+04<br><br> Pressure (bar)<br>
1.99809e+00 9.48448e-02 4.57909e-01<br> 7.74354e-02 4.97824e-01 1.84797e+00<br> 4.52125e-01 1.86535e+00 5.90776e-01<br><br> Total Dipole (D)<br>
-1.86272e+02 4.46310e+01 2.08554e+02<br><br> T-Protein T-non-Protein<br> 2.99904e+02 3.00013e+02<br><br><br> M E G A - F L O P S A C C O U N T I N G<br>
<br><br> There were in total 1502 frames (as shown in<br> VMD )...<br> I don't know about how it compared with the<br> coordinates of<br> the structure that I gave to grompp<br>
<br> --------<br><br> Pls guide<br><br><br><br><br> -- Bharat<br> Ph.D. Candidate<br> Room No. : 7202A, 2nd Floor<br>
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Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343
<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br></div></div></blockquote></div><br><br clear="all"><br>-- <br>Bharat<br>Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343
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