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Fro the majority of the analisys implemented in gromacs, you don't
need the tpr, a pdb and the xtc are ok.<br>
If you use the latest gromacs version (4.5.1) you need only the pdb
because gromacs is able to read each format vmd is able to read. <br>
To enable this feature, you have:<br>
1.Compiling gromacs with the flags "-L/usr/lib -ldl" <br>
2.At runtime setting the VMD_PLUGIN_PATH to the sub-directory
molfile of VMD<br>
<br>
If you do this, you can do:<br>
trjconv -f trajectpry.dcd -s file.pdb ........<br>
<br>
and the same with each tools<br>
<br>
Regarding conversion, I think editconf is the bestsolution<br>
<br>
<br>
<br>
<br>
<br>
Il 30/09/2010 22:57, oguz gurbulak ha scritto:
<blockquote cite="mid:703920.98510.qm@web36302.mail.mud.yahoo.com"
type="cite">
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<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="MsoNormal"><span style="font-family: Arial;
font-size: 11pt;">Dear All, <o:p></o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;"><o:p> </o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;">I think, In order to continue
a NAMD simulation in Gromacs I should first save the
last coordinates (.coor file in namd ) as a pdb file
and convert it into gro file . But there are many ways
to get a gro file <o:p></o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;"><o:p> </o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;">- using pdb2gmx ( but I
should choose the force field in gromacs. This may be
a problem. ) By the way, I changed CHARMM force field
and use Amber type force field in NAMD.<o:p></o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;"><o:p> </o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;">-using VMD ( but I’m not sure
if it works )<o:p></o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;"><o:p> </o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;">-using editconf in gromacs (
</span><span style="font-family: Arial; font-size:
11pt;" lang="EN">if you have the structure in pdb
format, you can convert it into a .gro file with
editconf. Also, the size of the box should be
specified (in gromacs the length for the vectors a, b
and c is in nm, not angstrom)<o:p></o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;"><o:p> </o:p></span></p>
<pre style="text-align: justify; background: none repeat scroll 0% 0% rgb(247, 247, 247);"><code><span style="font-family: Arial; font-size: 11pt;" lang="EN">editconf -f file.pdb -o file.gro -box a b c -angles 90 90 90</span></code><span style="font-family: Arial; font-size: 11pt;" lang="EN"><o:p></o:p></span></pre>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;"><o:p> </o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;">Could you share your ideas
about this process ? What should I do ?<o:p></o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;"><o:p> </o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;">Then I should convert the psf
file into gromacs top file. <o:p></o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;"><o:p> </o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;">If I get a gro and top file
correctly, I can continue NAMD simulation in Gromacs.
Is it true ?<o:p></o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;"><o:p> </o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;">I examined the gromacs
tutorials. And I think I must have a tpr and a xtc
file to use gromacs analysis tools. I can get a xtc
file from NAMD dcd file but how can I create a tpr
file ?<span style=""> </span>Is there a way to get a
tpr file from NAMD files? <o:p></o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810msonormal"><span style="font-family:
Arial; font-size: 11pt;"><o:p> </o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810yiv1079269607msonormal"><span
style="font-family: Arial; font-size: 11pt;"> <o:p></o:p></span>
</p>
<p style="text-align: justify; margin: 0cm 0cm 0pt;"
class="yiv1872873810yiv1079269607msonormal"><span
style="font-family: Arial; font-size: 11pt;">Kind
regards.<o:p></o:p></span><br>
<br>
--- On <b>Thu, 9/30/10, Roland Schulz <i><a class="moz-txt-link-rfc2396E" href="mailto:roland@utk.edu"><roland@utk.edu></a></i></b>
wrote:<br>
</p>
<blockquote style="border-left: 2px solid rgb(16, 16,
255); padding-left: 5px; margin-left: 5px;"><br>
From: Roland Schulz <a class="moz-txt-link-rfc2396E" href="mailto:roland@utk.edu"><roland@utk.edu></a><br>
Subject: Re: [gmx-users] NAMD simulation in Gromacs<br>
To: "Discussion list for GROMACS users"
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
Date: Thursday, September 30, 2010, 10:13 AM<br>
<br>
<div id="yiv2033235737"><br>
<br>
<div class="yiv2033235737gmail_quote">On Thu, Sep 30,
2010 at 7:55 AM, Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true"
href="http://us.mc363.mail.yahoo.com/mc/compose?to=mark.abraham@anu.edu.au"
rel="nofollow" target="_blank"
ymailto="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote style="border-left: 1px solid rgb(204,
204, 204); margin: 0px 0px 0px 0.8ex;
padding-left: 1ex;"
class="yiv2033235737gmail_quote">
<div class="yiv2033235737im"><br>
<br>
----- Original Message -----<br>
From: oguz gurbulak <<a
moz-do-not-send="true"
href="http://us.mc363.mail.yahoo.com/mc/compose?to=gurbulakoguz@yahoo.com"
rel="nofollow" target="_blank"
ymailto="mailto:gurbulakoguz@yahoo.com">gurbulakoguz@yahoo.com</a>><br>
Date: Thursday, September 30, 2010 21:38<br>
Subject: [gmx-users] NAMD simulation in Gromacs<br>
To: <a moz-do-not-send="true"
href="http://us.mc363.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org"
rel="nofollow" target="_blank"
ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<br>
</div>
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<p class="yiv2033235737MsoNormal"><font
style="background-color: rgb(245,
248, 240); font-style: normal;
font-size: 14px; font-weight:
normal;">> </font>Dear All,</p>
</div>
<p class="yiv2033235737MsoNormal">
</p>
<p style="text-align: justify;"
class="yiv2033235737MsoNormal">> I
performed a 50 ns md simulation using
NAMD and want to continue this
simulation for 10 ns in Gromacs. Is it
possible to continue a NAMD simulation
in Gromacs ? If so, could you please
give me the information about this
process ? <br>
</p>
<p style="text-align: justify;"
class="yiv2033235737MsoNormal"><br>
</p>
<p style="text-align: justify;"
class="yiv2033235737MsoNormal">Not
really. You would need to generate a
.top in the normal way, and this process
cannot use any topology information that
NAMD was using. You could start the
GROMACS simulation from the endpoint of
the NAMD simulation, but it would not be
continuous in any sense.<br>
</p>
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</blockquote>
<div><br>
</div>
<div>We have a patch to psfgen to generate gromacs
topology. We plan to put this on our website.
While it hasn't be uploaded yet, please write me
in case you would like to have a copy. It does
convert the parameter files. We use Pär's scripts
to do that part.</div>
<div> </div>
<blockquote style="border-left: 1px solid rgb(204,
204, 204); margin: 0px 0px 0px 0.8ex;
padding-left: 1ex;"
class="yiv2033235737gmail_quote">
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<div class="yiv2033235737im">
</div>
<p style="text-align: justify;"
class="yiv2033235737MsoNormal">Secondly
can I convert NAMD output files into
gromacs output files and use gromacs
analysis tools ? Could you please also
give me the information about this issue
?
</p>
<p class="yiv2033235737MsoNormal">
</p>
<p class="yiv2033235737MsoNormal">If you
have VMD installed then GROMACS is
supposed to be able to link to its
libraries to enable GROMACS tools to
read any file format that VMD can read,
which will include all NAMD formats. I'm
unaware that anybody has written any
documentation about this, however.
That's probably the path of least
resistance.</p>
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<div><br>
</div>
<div>Yes as long as VMD is installed (and GROMACS is
compiled with DLOPEN support - which is default)
all the GROMACS tools automatically can read most
VMD supported format. The exception is any format
which doesn't record the number of atoms (as e.g.
Amber).</div>
<div><br>
</div>
<div>Roland</div>
<div> </div>
</div>
</div>
<br>
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