From: Mauricio Carrillo Tripp (trippm_at_gmail.com)
Date: Thu Jul 21 2005 - 16:10:11 CDT
That's right, I also keep both 'charmm-formated' and 'namd-xplor-formated'
version of the same PSF file of the systems to use in either case,
although I generate both with charmm.
Let me know if that's what your problem was...
On 7/21/05, Chang, Christopher <Christopher_Chang_at_nrel.gov> wrote:
> Hi Mauricio,
> Thanks for responding. The formats of the PSF files are different
> between NAMD-generated and CHARMM-generated. I usually keep two PSF files
> for each system under study, one for CHARMM and one for NAMD. Now that you
> mention it, it looks like I'm using a NAMD PSF file with CHARMM for these QH
> analyses; I'll take a look to see if that makes a difference.
> -----Original Message-----
> *From:* Mauricio Carrillo Tripp [mailto:trippm_at_gmail.com]
> *Sent:* Thursday, July 21, 2005 1:05 PM
> *To:* Chang, Christopher
> *Cc:* namd-l_at_ks.uiuc.edu; justin_at_ks.uiuc.edu
> *Subject:* Re: namd-l: catdcd-generated files and CHARMM
> I've found that the best way to deal with these issues is to use the merge
> command from charmm itself, instead of using catdcd,
> and I haven't had any problems since then... BTW, I also 1) make the psf
> (xplor format) with charmm, then 2) run the simulation with
> namd, and 3) go back to charmm to analysis, but I don't know if the first
> step would make any difference in the third one.
> So far, this approach has worked for me.
> On 7/21/05, Chang, Christopher <Christopher_Chang_at_nrel.gov> wrote:
> > Hi,
> > I'm trying to use the quasiharmonic analysis facility of CHARMM to
> > analyze a trajectory created from multiple NAMD runs, then put together with
> > the catdcd utility. Although the number of coordinate sets in the file is
> > being seen correctly, I'm getting some other fishy output: "Time step was
> > 0.000000 AKMA time units.", as well as a string of binary characters in
> > what CHARMM interprets as the TITLE section of the DCD file.
> > Are NAMD DCD files compatible with CHARMM, and if so does the catdcd
> > utility to anyone's knowledge preserve this compatibility?
> > Thanks,
> > Chris
> > Christopher H. Chang, Ph.D.
> > Research Associate
> > National Renewable Energy Laboratory
> > 1617 Cole Blvd., Mail Stop 1608
> > Golden, CO 80401
> > Phone (303) 275-3751
> > Fax (303) 275-4007
> Mauricio Carrillo Tripp, PhD
> Department of Chemistry
> Wabash College
-- Mauricio Carrillo Tripp, PhD Department of Chemistry Wabash College trippm_at_wabash.edu http://trippm.bajacast.com/
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