Mark, <span class="gD" style="color:#790619">Tsjerk thanks!<br><br>I've check my uncompleated produced MD run by G_energy and find that average pressure is 1.1 Bar that is most close to ref.<br><br><br>By the way could you tell me about extra possible ways of checking running simmulation? ( E.g I'm calculating long produce trajectory and want to check my uncompleated system ).<br>
<br>As I understood One of the possible way is the ussage of G_energy but how I could obtain GRO and TPR file from uncompleated MD trajectory ( .trr) (recently I've asked about this but I've missed that topic ;o) ?<br>
<br><br><br>Thanks again<br><br>James<br></span><br><div class="gmail_quote">2011/11/25 Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<p>Hi James,</p>
<p>There have been extensive discussions about this on the list. Check the archives. In short, smaller systems give larger fluctuations, and shorter simulations give larger deviations from the expected average.</p>
<p>Cheers,</p>
<p>Tsjerk</p><font color="#888888">
</font><p></p><blockquote type="cite"><div><div></div><div class="h5">On Nov 25, 2011 7:23 AM, "James Starlight" <<a href="mailto:jmsstarlight@gmail.com" target="_blank">jmsstarlight@gmail.com</a>> wrote:<br>
<br>Dear Gromacs Users!<br><br><br>At the present time I'm simulating small peptide (11 a.c in coiled conformation) in water.<br>
<br>I've desided to use parameters from Lysozyme simmulation ( opls ff for parametrisation and all mdp parameters from that simulation).<br>
<br>Because my peptide was smaller than typical globular protein I've desided to use bigger periodical box than in tutorial<br><br>I've used editconf -c -d 1.5 -bt cubic instead of 1.0 nm in tutorial wich resulted in bigger box relative peptide size.<br>
<br>so i have this box vectors 5.39318 5.39318 5.39318<br><br>My experiment was in full agreement with the above tutorial until NVP phase was conducted. I have conducted 100ps equilibration but When I've checked average pressure it was 0.75 atm instead of 1 BAR and have big RMSD- 200. (also I've checked my system visually but it looks fine- I have not pointed any artifacts linked with unstable pressure like voids in the solvent etc). Should I equilibrate my sustem longer until pressure would not be stabilized to reference BAR? What another options should i take into account during simulation of the small peptides ?<br>
<br>Thanks,<br><br>James<br>
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