<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY><P>Thank you for your kind reply. I tried conjugate gradient but it is not running. It gives error that it can't prform conjugate gradient minimization.</P>
<P>Rahul Karyappa<BR></P><FONT face=Arial size=2>
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<TD><B><I>-- Original Message --</I></B><BR>From: <leafyoung81-group@yahoo.com><BR>To: Discussion list for GROMACS users <gmx-users@gromacs.org><BR>Date: Thu, 8 Sep 2005 05:41:31 -0700 (PDT)<BR>Subject: Re: [gmx-users] MDRUN errors<BR><BR><BR><BR><BR>--- Rahul Karyappa <r.karyappa@ncl.res.in> wrote:<BR><BR>><BR><BR>> Dear all,<BR>><BR><BR>> I created .gro and .top files for my structure<BR>> with<BR>> 48 repeat units of polymer surrounded by sodium ions<BR>> and water. First I<BR>> carried out energy minimization by steepest descents<BR>> and then I ran MD<BR>> for 2ps (40 steps). It runs upto 40 steps properly<BR>> and then it<BR>2/40 = 0.05ps = 50fs. Time step is too big for MD.<BR>Normally, 1 to 2fs.<BR>> starts giving errors as follows:<BR>><BR><BR>> starting mdrun 'Protein'<BR>><BR><BR>> 1000 steps, 2.0 ps.<BR>><BR><BR>><BR><BR>> step 40, remaining runtime: 23<BR>> s <BR><BR>> Warning: 1-4 interaction between 294 and 297 at<BR>> distance larger than 1<BR>> nm<BR>><BR><BR>> These are ignored for the rest of the simulation<BR>><BR><BR>> turn on -debug for more information<BR>><BR><BR>> step 50, remaining runtime: 18<BR>> s <BR><BR>> Wrote pdb files with previous and current<BR>> coordinates<BR>><BR><BR>> Wrote pdb files with previous and current<BR>> coordinates<BR>><BR><BR>><BR><BR>> Back Off! I just backed up step55.pdb to<BR>> ./#step55.pdb.1#<BR>><BR><BR>> Wrote pdb files with previous and current<BR>> coordinates<BR>><BR><BR>><BR><BR>> Back Off! I just backed up step56.pdb to<BR>> ./#step56.pdb.1#<BR>><BR><BR>> Wrote pdb files with previous and current<BR>> coordinates<BR>><BR><BR>> ...<BR>><BR><BR>> Back Off! I just backed up step60.pdb to<BR>> ./#step60.pdb.1#<BR>><BR><BR>> Wrote pdb files with previous and current<BR>> coordinates<BR>><BR><BR>> Fatal error: ci = -2147483648 should be in 0 .. 1330<BR>> [FILE nsgrid.c, LINE 218]<BR>><BR><BR>><BR><BR>> Also when I ran steepest descents the messages I got<BR>> were as follows:<BR>><BR><BR>><BR><BR>> Step= 44, Dmax= 1.2e-04 nm, Epot= -1.10077e+05<BR>> Fmax= 2.65510e+03, atom= 725<BR>><BR><BR>> Step= 52, Dmax= 1.1e-06 nm, Epot= -1.10077e+05<BR>> Fmax= 3.00823e+03, atom= 8860<BR>><BR><BR>> Stepsize too small, or no change in energy.<BR>><BR><BR>> Converged to machine precision,<BR>><BR><BR>> but not to the requested precision Fmax < 1000<BR>><BR><BR>><BR><BR>> Double precision normally gives you higher accuracy.<BR>><BR><BR>> You might need to increase your constraint accuracy,<BR>> or turn<BR>><BR><BR>> off constraints alltogether (set constraints = none<BR>> in mdp file)<BR>><BR><BR>><BR><BR>> writing lowest energy coordinates.<BR>><BR><BR>><BR><BR>> Back Off! I just backed up steep.trr to<BR>> ./#steep.trr.1#<BR>><BR><BR>><BR><BR>> Back Off! I just backed up steepout.gro to<BR>> ./#steepout.gro.1#<BR>><BR><BR>><BR><BR>> Steepest Descents converged to machine precision in<BR>> 53 steps,<BR>><BR><BR>> but did not reach the requested Fmax < 1000.<BR>><BR><BR>> Potential Energy = -1.1007694e+05<BR>><BR><BR>> Maximum force = 2.6551050e+03 on atom 725<BR>><BR><BR>> Norm of force = 1.0160128e+05<BR>><BR><BR>><BR>This is not an error. Try other em methods or proceed<BR>to equilibrium.<BR><BR>> Where am I going wrong? Please tell me. Thanking you<BR>> in advance.<BR>><BR><BR>><BR><BR>> Rahul Karyappa<BR>><BR><BR>> NCL, Pune<BR>><BR><BR>><BR><BR>><BR><BR>><BR><BR>><BR><BR>><BR><BR>><BR><BR>><BR>*****************************************************************<BR>> This email is virus free by TrendMicro Inter Scan<BR>> Security Suite.<BR>><BR>*****************************************************************><BR>_______________________________________________<BR>> gmx-users mailing list<BR>> gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please don't post (un)subscribe requests to the<BR>> list. Use the<BR><BR>> www interface or send it to<BR>gmx-users-request@gromacs.org.<BR><BR>_______________________________________________<BR>gmx-users mailing list<BR>gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please don't post (un)subscribe requests to the list. Use the<BR><BR>www interface or send it to gmx-users-request@gromacs.org.<BR><BR>*****************************************************************<BR>This email is virus free by TrendMicro Inter Scan Security Suite.<BR>*****************************************************************<BR></TD></TR></TBODY></TABLE></FONT></BODY></HTML>
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