<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt">Dear All, <?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></DIV>
<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv1872873810msonormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt"><o:p> </o:p></SPAN></DIV>
<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></DIV>
<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv1872873810msonormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt"><o:p> </o:p></SPAN></DIV>
<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></DIV>
<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv1872873810msonormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt"><o:p> </o:p></SPAN></DIV>
<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></DIV>
<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv1872873810msonormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt"><o:p> </o:p></SPAN></DIV>
<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; mso-ansi-language: EN" 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></DIV>
<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv1872873810msonormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt"><o:p> </o:p></SPAN></DIV><PRE style="TEXT-ALIGN: justify; BACKGROUND: #f7f7f7"><CODE><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt; mso-ansi-language: EN" 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; mso-ansi-language: EN" 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></DIV>
<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></DIV>
<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv1872873810msonormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt"><o:p> </o:p></SPAN></DIV>
<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></DIV>
<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv1872873810msonormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt"><o:p> </o:p></SPAN></DIV>
<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></DIV>
<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv1872873810msonormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt"><o:p> </o:p></SPAN></DIV>
<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="mso-spacerun: yes"> </SPAN>Is there a way to get a tpr file from NAMD files? <o:p></o:p></SPAN></DIV>
<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv1872873810msonormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt"><o:p> </o:p></SPAN></DIV>
<P style="TEXT-ALIGN: justify; MARGIN: 0cm 0cm 0pt" class=yiv1872873810yiv1079269607msonormal><SPAN style="FONT-FAMILY: Arial; FONT-SIZE: 11pt"> <o:p></o:p></SPAN></DIV>
<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></DIV><BR><BR>--- On <B>Thu, 9/30/10, Roland Schulz <I><roland@utk.edu></I></B> wrote:<BR>
<BLOCKQUOTE style="BORDER-LEFT: rgb(16,16,255) 2px solid; PADDING-LEFT: 5px; MARGIN-LEFT: 5px"><BR>From: Roland Schulz <roland@utk.edu><BR>Subject: Re: [gmx-users] NAMD simulation in Gromacs<BR>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Date: Thursday, September 30, 2010, 10:13 AM<BR><BR>
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<DIV class=yiv2033235737gmail_quote>On Thu, Sep 30, 2010 at 7:55 AM, Mark Abraham <SPAN dir=ltr><<A 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>
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<DIV class=yiv2033235737im><BR><BR>----- Original Message -----<BR>From: oguz gurbulak <<A 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 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,</DIV>
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<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></DIV>
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<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></DIV></TD></TR></TBODY></TABLE></BLOCKQUOTE>
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<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>
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<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 ?</DIV>
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<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.</DIV></TD></TR></TBODY></TABLE></BLOCKQUOTE>
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<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>
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<DIV>Roland</DIV>
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