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<P><FONT SIZE=2>Thanks for your reply.<BR>
a) energy minimized well with double precision<BR>
How well?<BR>
potential energy =-4.something<BR>
<BR>
b) system net charge = -22.816e<BR>
This is wrong, check topology.<BR>
Sorry typo -2.816e<BR>
<BR>
c) electrostatic method = cut-off<BR>
What cut-off? 20 A<BR>
<BR>
<BR>
<BR>
<BR>
Abu Naser<BR>
PhD Student<BR>
School Of Life Sciences<BR>
Heriot-Watt University<BR>
Edinburgh<BR>
EH14 4AS<BR>
Email: mn2@hw.ac.uk<BR>
Phone: +44(0)1314518265<BR>
Mobile:+44(0)7814877110<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmx-users-bounces@gromacs.org on behalf of David<BR>
Sent: Mon 9/19/2005 5:19 PM<BR>
To: Discussion list for GROMACS users<BR>
Subject: Re: [gmx-users] (no subject)<BR>
<BR>
On Mon, 2005-09-19 at 17:06 +0100, Naser, Md Abu wrote:<BR>
> Hi All,<BR>
><BR>
><BR>
> ASSUMTION: Bad starting structure<BR>
><BR>
> PROBLEM: 1-4 interaction longer than.../large velocity of center of<BR>
> mass<BR>
><BR>
> FACTS:<BR>
> a) energy minimized well with double precision<BR>
How well?<BR>
<BR>
> b) system net charge = -22.816e<BR>
This is wrong, check topology.<BR>
<BR>
> c) electrostatic method = cut-off<BR>
What cut-off?<BR>
<BR>
><BR>
> TRIED AND FAILED: setting LOGBUFS=0<BR>
> <BR>
><BR>
> INFORMATION SHOUGHT :<BR>
> possible ways to resolve the problem<BR>
><BR>
> With regards,<BR>
> Abu Naser<BR>
> PhD Student<BR>
> School Of Life Sciences<BR>
> Heriot-Watt University<BR>
> Edinburgh<BR>
> EH14 4AS<BR>
> Email: mn2@hw.ac.uk<BR>
> Phone: +44(0)1314518265<BR>
> Mobile:+44(0)7814877110<BR>
><BR>
><BR>
> _______________________________________________<BR>
> gmx-users mailing list<BR>
> gmx-users@gromacs.org<BR>
> <A HREF="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>
> Please don't post (un)subscribe requests to the list. Use the<BR>
> www interface or send it to gmx-users-request@gromacs.org.<BR>
--<BR>
David.<BR>
________________________________________________________________________<BR>
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<BR>
Dept. of Cell and Molecular Biology, Uppsala University.<BR>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>
phone: 46 18 471 4205 fax: 46 18 511 755<BR>
spoel@xray.bmc.uu.se spoel@gromacs.org <A HREF="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</A><BR>
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