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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:<br>
<br>
do_dssp -s md.tpr -f md.trr -b 100 -e 200 -f ss.xpm<br>
<br>
<br>
On 03/30/2012 03:05 PM, Erik Marklund wrote:
<blockquote
cite="mid:9FC2E7D7-75BC-4828-959F-3D4000BB75D6@xray.bmc.uu.se"
type="cite">And what versions were those?
<div><br>
<div>
<div>30 mar 2012 kl. 15.06 skrev Albert:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div>I've tried different kind of DSSP version, but the
problem is the same....<br>
<br>
<br>
On 03/30/2012 02:54 PM, <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>
wrote:<br>
<blockquote type="cite">Send gmx-users mailing list
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<blockquote type="cite">To subscribe or unsubscribe via
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<blockquote type="cite">You can reach the person managing
the list at<br>
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<blockquote type="cite"><span class="Apple-tab-span"
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</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">When replying, please edit your
Subject line so it is more specific<br>
</blockquote>
<blockquote type="cite">than "Re: Contents of gmx-users
digest..."<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Today's Topics:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"> 1. Re: Re: do_dssp error (Erik
Marklund)<br>
</blockquote>
<blockquote type="cite"> 2. Re: Not able to continue
with Equilibration (Justin A. Lemkul)<br>
</blockquote>
<blockquote type="cite"> 3. Re: HB lifetime (Nidhi
Katyal)<br>
</blockquote>
<blockquote type="cite"> 4. Re: HB lifetime (Justin A.
Lemkul)<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">----------------------------------------------------------------------<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Message: 1<br>
</blockquote>
<blockquote type="cite">Date: Fri, 30 Mar 2012 13:28:05
+0200<br>
</blockquote>
<blockquote type="cite">From: Erik Marklund<<a
moz-do-not-send="true"
href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>><br>
</blockquote>
<blockquote type="cite">Subject: Re: [gmx-users] Re:
do_dssp error<br>
</blockquote>
<blockquote type="cite">To: Discussion list for GROMACS
users<<a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
</blockquote>
<blockquote type="cite">Message-ID:<<a
moz-do-not-send="true"
href="mailto:129A1E28-ABBD-4733-BA85-C1F6B2F4BE89@xray.bmc.uu.se">129A1E28-ABBD-4733-BA85-C1F6B2F4BE89@xray.bmc.uu.se</a>><br>
</blockquote>
<blockquote type="cite">Content-Type: text/plain;
charset="us-ascii"<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">And I replied "What's your dssp
version? The most recent ones have different flags that
are not yet supported by gromacs."<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Erik<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">30 mar 2012 kl. 13.23 skrev
Albert:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Hello:<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"> there is some problem for my
do_dssp, it always claimed:<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Program do_dssp_d, VERSION 4.5.5<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Source code file: do_dssp.c,
line: 572<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Fatal error:<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Failed to execute command:
/usr/local/bin/dssp -na ddg1g7Id ddRwthIi>
/dev/null 2> /dev/null<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">someone suggest to compile
gromacs with double precision and I recompiled it with
--enable-double<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">but it still doesn't work.....<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">does anybody else have any
suggestions?<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">THX<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">-- <br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">gmx-users mailing list <a
moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Please search the archive at <a
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href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Please don't post (un)subscribe
requests to the list. Use the www interface or send it
to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Can't post? Read <a
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href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote>
</blockquote>
<blockquote type="cite">-----------------------------------------------<br>
</blockquote>
<blockquote type="cite">Erik Marklund, PhD<br>
</blockquote>
<blockquote type="cite">Dept. of Cell and Molecular
Biology, Uppsala University.<br>
</blockquote>
<blockquote type="cite">Husargatan 3, Box 596, 75124
Uppsala, Sweden<br>
</blockquote>
<blockquote type="cite">phone: +46 18 471 6688
fax: +46 18 511 755<br>
</blockquote>
<blockquote type="cite"><a moz-do-not-send="true"
href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a><br>
</blockquote>
<blockquote type="cite"><a moz-do-not-send="true"
href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">-------------- next part
--------------<br>
</blockquote>
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<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">------------------------------<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Message: 2<br>
</blockquote>
<blockquote type="cite">Date: Fri, 30 Mar 2012 08:26:05
-0400<br>
</blockquote>
<blockquote type="cite">From: "Justin A. Lemkul"<<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
</blockquote>
<blockquote type="cite">Subject: Re: [gmx-users] Not able
to continue with Equilibration<br>
</blockquote>
<blockquote type="cite">To: Discussion list for GROMACS
users<<a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
</blockquote>
<blockquote type="cite">Message-ID:<<a
moz-do-not-send="true"
href="mailto:4F75A65D.1040701@vt.edu">4F75A65D.1040701@vt.edu</a>><br>
</blockquote>
<blockquote type="cite">Content-Type: text/plain;
charset=ISO-8859-1; format=flowed<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">francesca vitalini wrote:<br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Dear Mark,<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Thank you for your answer. I'm
trying now with the position restraints<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">and see what happens.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">However, another question came
up to my mind in the mean time. I'm<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">using GROMACS 3.3.1 (version
with mapping for reverse transformation,<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">I have been posting on it
before) and for the mdrun the flag -coarse<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">is required. From the mdrun -h
help, the -coarse flag resulted to be a<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">generic trajectory, so I assumed
it was needed for the names of the<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">atoms or something similar.
However, trying to run the nvt.mdp with<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">the original coarse grained file
specified for this flag, resulted in<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">the simulation not dying at the
very first steps.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"> I'm not sure if it will work
out eventually ( the 20 ps simulations<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">is supposed to finish in 12
hours, which is still kind of worrying<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">despite my system being pretty
big) but definitely told me that the<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">-coarse flag might be of
fundamental importance.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Unfortunately I couldn't find
any more detailed documentation about it.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Could anyone explain to me what
it does or point me to where to find<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">the related documentation?<br>
</blockquote>
</blockquote>
<blockquote type="cite">Where did you obtain this version
of Gromacs? You're not using an official<br>
</blockquote>
<blockquote type="cite">version, so you're not likely to
find its documentation in the usual places and<br>
</blockquote>
<blockquote type="cite">it's very hard for this community
to help you using a modified version of<br>
</blockquote>
<blockquote type="cite">antiquated software. You're more
likely to have luck contacting whoever created<br>
</blockquote>
<blockquote type="cite">these modifications for help,
since potential problems with code stability and<br>
</blockquote>
<blockquote type="cite">performance are likely best
addressed by those who made the modifications.<br>
</blockquote>
<blockquote type="cite">Perhaps they are members of this
list, but contacting them directly is probably<br>
</blockquote>
<blockquote type="cite">a better approach.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">-Justin<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
</div>
</blockquote>
</div>
<br>
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<div style="word-wrap: break-word; -webkit-nbsp-mode:
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<div>-----------------------------------------------</div>
<div>Erik Marklund, PhD</div>
<div>Dept. of Cell and Molecular Biology, Uppsala
University.</div>
<div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div>
<div>phone: +46 18 471 6688 fax: +46 18
511 755</div>
<div><a moz-do-not-send="true"
href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div>
<div><a moz-do-not-send="true"
href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div>
</div>
</span></div>
</span></span> </div>
<br>
</div>
</blockquote>
<br>
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