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<div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"><div id="yiv125690666"><div><div style="color:#000;background-color:#fff;font-family:arial, helvetica, sans-serif;font-size:12pt;"><div><span>One more question:</span></div><div><span>But what about of using the potential surface?</span></div><div><span>In fact, I want to use the results of modeling in umbrella sampling. Is it possible?</span></div><div><br><span></span></div><div><span>Thanks in advance,</span></div><div><span>Shima <br></span></div><div><br></div> <div style="font-family:arial, helvetica, sans-serif;font-size:12pt;"> <div style="font-family:times new roman, new york, times, serif;font-size:12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Peter C. Lai <pcl@uab.edu><br> <b><span
style="font-weight:bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight:bold;">Sent:</span></b> Monday, April 16, 2012 9:50 PM<br>
<b><span style="font-weight:bold;">Subject:</span></b> Re: [gmx-users] GROMOS87 and CHARMM27<br> </font> </div> <br>
On 2012-04-16 10:14:01AM -0700, Shima Arasteh wrote:<br>> So, I can not use the coordinates of the output files of gromos runs. Right?<br><br>You can but you may need to rename the atoms for each residue for pdb2gmx<br>to work.<br><br>> <br>> <br>> ________________________________<br>> From: Peter C. Lai <<a rel="nofollow" ymailto="mailto:pcl@uab.edu" target="_blank" href="mailto:pcl@uab.edu">pcl@uab.edu</a>><br>> To: Discussion list for GROMACS users <<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>> <br>> Sent: Monday, April 16, 2012 8:23 PM<br>> Subject: Re: [gmx-users] GROMOS87 and CHARMM27<br>> <br>> On 2012-04-16 08:26:00AM -0700, Shima Arasteh wrote:<br>> > Dear GROMACS users,<br>> > <br>> > I reproduced the results of a protein-membrane system by using force field GROMOSE87. This protein
forms ion channel in membrane.<br>> > Now if I wanna study
the ion conduction through this channel using force field CHARMM27 in umbrella sampling method, is it possible? Can I use the results of the system simulation which has been derived by GROMOS87?<br>> <br>> By definition, switching to a different forcefield like that usually requires <br>> the regeneration of the system's topology, so your new system will be <br>> different from your old one anyway. In addition, you may need to rename the <br>> atoms in the coordinate files obtained from previous gromos runs to match <br>> those in the charmm27 residue files.<br>> <br>> -- <br>> ==================================================================<br>> Peter C. Lai | University of Alabama-Birmingham<br>> Programmer/Analyst | KAUL 752A<br>> Genetics, Div. of Research | 705 South 20th Street<br>> <a
rel="nofollow" ymailto="mailto:pcl@uab.edu" target="_blank" href="mailto:pcl@uab.edu">pcl@uab.edu</a> | Birmingham AL 35294-4461<br>> (205) 690-0808 |<br>> ==================================================================<br>> <br>> -- <br>> gmx-users mailing list <a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at <a rel="nofollow" target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to <a rel="nofollow"
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