VMD-L Mailing List

From: Jerry Xu (jerryx_at_hotmail.com)
Date: Thu Jul 15 2004 - 14:50:51 CDT

Thanks, Bogdan, you are right, I noticed that psfgen put into everything
into one group. Because I am really new to both psfgen and charmm, I am just
wondering how I can put these atoms into several groups--- through some
commands either from psfgen or from charmm. That is also what I initially
try to get solution for this matter by posting question here. The other
person kindly suggest me re-compile charmm with large or xxlarge
limitation..... hope that works, I have not tried yet.

Thanks again.

>From: Bogdan Costescu <bogdan.costescu_at_IWR.Uni-Heidelberg.De>
>To: Jerry Xu <jerryx_at_hotmail.com>
>CC: vmd-l_at_ks.uiuc.edu, <yxu3_at_lsu.edu>
>Subject: Re: vmd-l: vmd psfgen problem with CHARMM
>Date: Thu, 15 Jul 2004 20:46:26 +0200 (CEST)
>
>On Thu, 15 Jul 2004, Jerry Xu wrote:
>
> > ***** LEVEL -3 WARNING FROM <MAKGRP> *****
> > ***** maximum number of atoms per group exceeded
>
>OK, so this comes from the nonbonded exclusion calculations. The
>parameter that is checked against is defined as:
>
>"The maximum number of atoms in any electrostatic group"
>
>and has a value of 1000 (MAXING in source/fcm/dimens.fcm). And when
>you look earlier in the output (reformatted to avoid line wrap):
>
> Number of atoms = 1569 Number of groups = 1
>
>So you are asking CHARMM to put all your 1569 atoms in one group and
>this fails. Is this your (or psfgen's) intention ? When I did
>calculations when CHARMM I used to have an average of 3-4 atoms per
>group...
>
>--
>Bogdan Costescu
>
>IWR - Interdisziplinaeres Zentrum fuer Wissenschaftliches Rechnen
>Universitaet Heidelberg, INF 368, D-69120 Heidelberg, GERMANY
>Telephone: +49 6221 54 8869, Telefax: +49 6221 54 8868
>E-mail: Bogdan.Costescu_at_IWR.Uni-Heidelberg.De
>
>

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