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Hi,<br><br>Do not "randomly" change the fourierspacing.<br>Are you really using PME in vacuum?<br><br>The box size can only change if you have pressure coupling turned on,<br>which should, obviously, should not do in vacuum.<br><br>Berk<br><br><hr id="stopSpelling">Date: Thu, 8 Oct 2009 15:13:25 +0530<br>From: pdnikhil@yahoo.co.in<br>Subject: Re: [gmx-users] Load imbalance and Y size error<br>To: gmx-users@gromacs.org<br><br>
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</style><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div>Now when i increased the fourierspacing from 0.12 to 0.22 nm, it worked properly on single node and failed on multiple nodes giving same error of<br>"The Y-size of the box (4.612312) times the triclinic skew factor (0.866052) is smaller than the number of DD cells (2) times the smallest allowed cell size(2.000000)"<br><br>What possibly could be the reason ? <br><br>Regards,<br>Nikhil<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> nikhil damle <pdnikhil@yahoo.co.in><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users
<gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Thu, 8 October, 2009 2:10:04 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Load imbalance and Y size error<br></font><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div>No. My system is a single protein with charged ligand associated with it. But why should box size shrink ? In solvated system it does not shrink. What effect vacuum could possibly have on it ?<br><br>Regards,<br>Nikhil<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br><b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Thu, 8 October, 2009 12:46:56 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re:
[gmx-users] Load imbalance and Y size error<br></font><br>nikhil damle wrote:<br>> Hi,<br>> <br>> I tried to run on single node now. Now the error is different saying<br>> "One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off"<br>> <br>> This means that my box shrinks during dynamics (this is not constant volume MD) But when Solvent is present in the same system, this does not happen. How should i deal with it then ?<br><br>If it's not constant volume then the simulation will change volume. Why should your charged proteins want to stay at the original distance from each other? It seems they want to collapse onto each other. You need to rethink your choice of ensemble.<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a rel="nofollow" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a rel="nofollow" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a rel="nofollow" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a rel="nofollow" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a rel="nofollow" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></div></div></div><br>
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