<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><br><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="yiv1183257467"><div><div style="color:#000;background-color:#fff;font-family:arial, helvetica, sans-serif;font-size:12pt;"><div><span>Dear Justin,</span></div><div><span>I don't want to compare the forcefields results.</span></div><div><span>Yes, </span>Iwant to use some old information in conjunction with something new.</div><div><span>In fact, I have to regenerate a structure, which has modulated using gmx.ff. After it, I am going to study it using umbrella sampling technique. I want to do it using charmm27. I want to know if it is possible? Is it correct that I use the results of the job done by gmx? Or I need to repeat the job using
charmm?</span></div><div><br><span></span></div><div><span>Thanks,</span></div><div><span>Shima</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> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight:bold;">To:</span></b> Shima Arasteh <shima_arasteh2001@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight:bold;">Sent:</span></b> Tuesday, May 1, 2012 9:44 PM<br> <b><span style="font-weight:bold;">Subject:</span></b> Re: Fw: [gmx-users] GROMOS87 and CHARMM27<br> </font> </div> <br>
<br><br>On 5/1/12 1:08 PM, Shima Arasteh wrote:<br>><br>><br>> One more question:<br>> But what about of using the potential surface?<br>> In fact, I want to use the results of modeling in umbrella sampling. Is it possible?<br>><br><br>I, for one, am not clear what you are asking. Are you trying to compare force <br>field results? Build a system based off another? Use some old information in <br>conjunction with something new (i.e. force field mixing, which is a bad idea)?<br><br>-Justin<br><br>> Thanks in advance,<br>> Shima<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 9:50 PM<br>> *Subject:* Re: [gmx-users] GROMOS87 and CHARMM27<br>><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> <mailto:<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>> <mailto:<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<br>> GROMOSE87. This protein forms ion channel in membrane.<br>> > > Now if I wanna study the ion conduction through this channel using force<br>> field CHARMM27 in umbrella sampling method, is it possible? Can I use the<br>> 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> <mailto:<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
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http://www.gromacs.org/Support/Mailing_Lists<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> <mailto:<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> > <a rel="nofollow" target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> > Please search the archive at<br>> <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"
ymailto="mailto:gmx-users-request@gromacs.org" target="_blank" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>>
<mailto:<a rel="nofollow" ymailto="mailto:gmx-users-request@gromacs.org" target="_blank" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> > Can't post? Read <a rel="nofollow" target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br>><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> <mailto:<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> <mailto:<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <a rel="nofollow" target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><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><br>> 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" ymailto="mailto:gmx-users-request@gromacs.org" target="_blank"
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>> <mailto:<a rel="nofollow" ymailto="mailto:gmx-users-request@gromacs.org" target="_blank" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a rel="nofollow" target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br>><br>><br>><br>><br>><br>><br><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a rel="nofollow" target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br><br><br> </div> </div>
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