<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Justin,<br></blockquote></div></blockquote><div><br>I was looking all the time for a file with dgdl extension throughout the directory. IIRC in previous versions -dgdl would generate such extension. I found now .xvg file which has dhdl data. (if I am right dgdl is the very dhdl in 4.5.3!) <br>
</div><div><br> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I have a little problem with FE output file. Below is the settings and also I am including -dgdl in the command I issue but no dgdl (or dhdl) file generates. I dont figure where the problem lies ! (version 4.5.3).<br>
<br>
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How long has the simulation been running? Output is buffered, and I find that dhdl.xvg is not updated often.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
free_energy = yes<br>
init_lambda = 0 delta_lambda = 0<br>
sc_alpha = 0.5<br>
sc-power = 1<br>
sc_sigma = 0.3<br>
foreign_lambda = 0.1<br>
dhdl_derivatives = yes<br>
couple-moltype = Polymer<br>
couple-lambda0 = vdw-q couple-lambda1 = none<br>
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Note that turning off all interactions simultaneously (especially when using soft-core) can be very unstable. You should (de)couple vdW and Coulombic interactions separately.<br></blockquote><div><br>Yes I read your comment about decoupling separately earlier on but I was not sure if this could depend upon the system so I was thinking of comparing results from two trials: <br>
<br>trial 1:<br>couple-lambda0 = vdw-q <br>couple-lambda1 = none <br><br> trail 2 A:<br>couple-lambda0 = vdw-q <br>couple-lambda1 = vdw<br> trail 2 B<br>couple-lambda0 = vdw<br>
couple-lambda1 = none <br><br></div><div>So: <br><br>1- Does this decoupling issue depend on the system or it is a must for all FE studies?<br>2- I actually went through many of FE posts and never found how separete decoupling can be done. from trail 2 A and B I get dgdl files but how to get total vdw-q to none from these two? Please shed some light on the details of procedure..<br>
<br>3- With free_energy turned off my runs take only a few hours but as I shift to free_energy = yes, runs take nearly one day foe each lambda.. Is this normal for s system having 2500 atoms? <br> <br> Thanks<br>
</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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Best<br>
<br>
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-- <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>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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