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Today's Topics:
1. Re: Re: do_dssp error (Erik Marklund)
2. Re: Not able to continue with Equilibration (Justin A. Lemkul)
3. Re: HB lifetime (Nidhi Katyal)
4. Re: HB lifetime (Justin A. Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Fri, 30 Mar 2012 13:28:05 +0200
From: Erik Marklund<[email protected] <mailto:[email protected]>>
Subject: Re: [gmx-users] Re: do_dssp error
To: Discussion list for GROMACS users<[email protected]
<mailto:[email protected]>>
Message-ID:<[email protected]
<mailto:[email protected]>>
Content-Type: text/plain; charset="us-ascii"
And I replied "What's your dssp version? The most recent ones have
different flags that are not yet supported by gromacs."
Erik
30 mar 2012 kl. 13.23 skrev Albert:
Hello:
there is some problem for my do_dssp, it always claimed:
Program do_dssp_d, VERSION 4.5.5
Source code file: do_dssp.c, line: 572
Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddg1g7Id
ddRwthIi> /dev/null 2> /dev/null
someone suggest to compile gromacs with double precision and I
recompiled it with --enable-double
but it still doesn't work.....
does anybody else have any suggestions?
THX
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 6688 fax: +46 18 511 755
[email protected] <mailto:[email protected]>
http://www2.icm.uu.se/molbio/elflab/index.html
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Message: 2
Date: Fri, 30 Mar 2012 08:26:05 -0400
From: "Justin A. Lemkul"<[email protected] <mailto:[email protected]>>
Subject: Re: [gmx-users] Not able to continue with Equilibration
To: Discussion list for GROMACS users<[email protected]
<mailto:[email protected]>>
Message-ID:<[email protected] <mailto:[email protected]>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
francesca vitalini wrote:
Dear Mark,
Thank you for your answer. I'm trying now with the position restraints
and see what happens.
However, another question came up to my mind in the mean time. I'm
using GROMACS 3.3.1 (version with mapping for reverse transformation,
I have been posting on it before) and for the mdrun the flag -coarse
is required. From the mdrun -h help, the -coarse flag resulted to be a
generic trajectory, so I assumed it was needed for the names of the
atoms or something similar. However, trying to run the nvt.mdp with
the original coarse grained file specified for this flag, resulted in
the simulation not dying at the very first steps.
I'm not sure if it will work out eventually ( the 20 ps simulations
is supposed to finish in 12 hours, which is still kind of worrying
despite my system being pretty big) but definitely told me that the
-coarse flag might be of fundamental importance.
Unfortunately I couldn't find any more detailed documentation about it.
Could anyone explain to me what it does or point me to where to find
the related documentation?
Where did you obtain this version of Gromacs? You're not using an
official
version, so you're not likely to find its documentation in the usual
places and
it's very hard for this community to help you using a modified
version of
antiquated software. You're more likely to have luck contacting
whoever created
these modifications for help, since potential problems with code
stability and
performance are likely best addressed by those who made the
modifications.
Perhaps they are members of this list, but contacting them directly
is probably
a better approach.
-Justin
