<div>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 .. </div>
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<div class="gmail_quote">On Thu, Jan 27, 2011 at 3:44 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<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 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 ..<br>
<br></blockquote><br></div>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.<br><br>You can save more frequently by setting the proper output controls. Read in the manual about the nst* options and set the accordingly.<br>
<br>-Justin<br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div>On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul <<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 * <<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a><br></div>
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<div> <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 asking ..<br> since I am not an expert with gromacs..<br>
<br><br> Please leave the old context for the discussion in future<br> emails. Only you are paying so much attention to your work that<br> you can be sure of remembering things :-)<br><br> If your simulation started with these strands unfolded, then<br>
your problem is somewhere else. However, you have to be able to<br> tell us what was the initial conformation, and when your "first<br> trajectory frame" (per last email) happened in the simulation.<br>
<br><br> I would also add that VMD does a fairly poor job sometimes of<br> guessing secondary structure. So if no beta strand was present in<br> the very first frame, that doesn't necessarily mean the secondary<br>
structure wasn't stable, it just means VMD didn't display it properly.<br><br> -Justin<br><br> Mark<br><br><br> I don't know when is was written .. Here are 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 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 VMD )...<br> I don't know about how it compared with the 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> 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<br>
Mobile no. - 010-5818-3680<br> E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a> <mailto:<a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a>><br>
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<div><br><br><br> -- ========================================<br><br> Justin A. Lemkul<br> Ph.D. Candidate<br> ICTAS Doctoral Scholar<br> MILES-IGERT Trainee<br> Department of Biochemistry<br> Virginia Tech<br>
Blacksburg, VA<br></div> jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> <<a href="http://vt.edu/" target="_blank">http://vt.edu</a>> | (540) 231-9080
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<div><br> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br><br><br><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<br>Mobile no. - 010-5818-3680<br>
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<div><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br>
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</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
<div>Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>