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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="stopSpelling">> From: gmx3@hotmail.com<br>> To: gmx-users@gromacs.org<br>> Date: Thu, 31 Jan 2008 15:56:01 +0100<br>> Subject: [gmx-users] RE: RE : FEP : separating components of dgdl<br>> <br>> <br>> <br>> <br>> ----------------------------------------<br>> > Date: Thu, 31 Jan 2008 15:29:50 +0100<br>> > From: michael.bon@cea.fr<br>> > To: gmx-users@gromacs.org<br>> > Subject: RE : FEP : separating components of dgdl<br>> > <br>> > Hi,<br>> > <br>> > You were right for the bonds, I forgot that I was using constraints = all-bonds.<br>> > <br>> > Could the missing term be the soft core then ? Or is it included in VdW ?<br>> > <br>> No, those terms are always included.<br>> <br>> > Anyway, I noticed that this problem of hidden extra term happens when I modify something else than a hydrogen. Does it make sense ?<br>> > For example, I did N->DUM with all the parameters kept the same : every components of dVdl are 0 (VdW, Coulomb, angle, proper dihedral, Ryck., LJ 1-4, position restraint, disp. corr. ), but dVdl/dlambda is -6. Any idea ?<br>> <br>> I have no clue.<br>> But the easy way to find out is to take your system with only N->DUM<br>> and do two runs of zero steps at two different lambda values and see which energy term<br>> in the log file has changed.<br><br>I just realized that the constraint contribution to dVdl is not printed.<br>In MD this contribution is actually partially dVdl and partially dEkindl, but Gromacs adds it to dVdl.<br>But you say that you kept everything the same.<br>Are you sure your bond/constraint lengths did not change?<br>You can check this easily with gmxcheck -s1 -ab<br><br>Berk.<br><br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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