[gmx-users] Re: gmx-users Digest, Vol 95, Issue 208

Fri Mar 30 16:38:18 CEST 2012

I've tried: 2, 2.1.3, 2.1.4, the problem is still there. I don't think 
the do_dssp is so difficult. just one command:

do_dssp -s md.tpr -f md.trr -b 100 -e 200 -f ss.xpm

On 03/30/2012 03:05 PM, Erik Marklund wrote:
> And what versions were those?
>
> 30 mar 2012 kl. 15.06 skrev Albert:
>
>> I've tried different kind of DSSP version, but the problem is the 
>> same....
>>
>>
>> On 03/30/2012 02:54 PM, gmx-users-request at gromacs.org 
>> <mailto:gmx-users-request at gromacs.org> wrote:
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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<erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>>
>>> Subject: Re: [gmx-users] Re: do_dssp error
>>> To: Discussion list for GROMACS users<gmx-users at gromacs.org 
>>> <mailto:gmx-users at gromacs.org>>
>>> Message-ID:<129A1E28-ABBD-4733-BA85-C1F6B2F4BE89 at xray.bmc.uu.se 
>>> <mailto:129A1E28-ABBD-4733-BA85-C1F6B2F4BE89 at xray.bmc.uu.se>>
>>> 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
>>>> -- 
>>>> gmx-users mailing list gmx-users at gromacs.org 
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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
>>> erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>
>>> 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"<jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>> Subject: Re: [gmx-users] Not able to continue with Equilibration
>>> To: Discussion list for GROMACS users<gmx-users at gromacs.org 
>>> <mailto:gmx-users at gromacs.org>>
>>> Message-ID:<4F75A65D.1040701 at vt.edu <mailto:4F75A65D.1040701 at vt.edu>>
>>> 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
>>>
>
> -----------------------------------------------
> 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
> erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>
> http://www2.icm.uu.se/molbio/elflab/index.html
>

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