<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 &lt;jalemkul@vt.edu&gt;<br> <b><span style="font-weight:bold;">To:</span></b> Shima Arasteh &lt;shima_arasteh2001@yahoo.com&gt;; Discussion list for GROMACS users &lt;gmx-users@gromacs.org&gt; <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>&gt;<br>&gt;<br>&gt; One more question:<br>&gt; But what about of using the potential surface?<br>&gt; In fact, I want to use the results of modeling in umbrella sampling. Is it possible?<br>&gt;<br><br>I, for one, am not clear what you are asking.&nbsp; Are you trying to compare force <br>field results?&nbsp; Build a system based off another?&nbsp; 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>&gt; Thanks in advance,<br>&gt; Shima<br>&gt;<br>&gt; --------------------------------------------------------------------------------<br>&gt; *From:* Peter C. Lai &lt;<a rel="nofollow" ymailto="mailto:pcl@uab.edu" target="_blank" href="mailto:pcl@uab.edu">pcl@uab.edu</a>&gt;<br>&gt; *To:* Discussion list for GROMACS users &lt;<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank"
 href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>&gt;<br>&gt; *Sent:* Monday,
 April 16, 2012 9:50 PM<br>&gt; *Subject:* Re: [gmx-users] GROMOS87 and CHARMM27<br>&gt;<br>&gt; On 2012-04-16 10:14:01AM -0700, Shima Arasteh wrote:<br>&gt;&nbsp; &gt; So, I can not use the coordinates of the output files of gromos runs. Right?<br>&gt;<br>&gt; You can but you may need to rename the atoms for each residue for pdb2gmx<br>&gt; to work.<br>&gt;<br>&gt;&nbsp; &gt;<br>&gt;&nbsp; &gt;<br>&gt;&nbsp; &gt; ________________________________<br>&gt;&nbsp; &gt; From: Peter C. Lai &lt;<a rel="nofollow" ymailto="mailto:pcl@uab.edu" target="_blank" href="mailto:pcl@uab.edu">pcl@uab.edu</a> &lt;mailto:<a rel="nofollow" ymailto="mailto:pcl@uab.edu" target="_blank" href="mailto:pcl@uab.edu">pcl@uab.edu</a>&gt;&gt;<br>&gt;&nbsp; &gt; To: Discussion list for GROMACS users &lt;<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>&gt; &lt;mailto:<a rel="nofollow"
 ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>&gt;&gt;<br>&gt;&nbsp; &gt; Sent: Monday, April 16, 2012 8:23 PM<br>&gt;&nbsp; &gt; Subject: Re: [gmx-users] GROMOS87 and CHARMM27<br>&gt;&nbsp; &gt;<br>&gt;&nbsp; &gt; On 2012-04-16 08:26:00AM -0700, Shima Arasteh wrote:<br>&gt;&nbsp; &gt; &gt; Dear GROMACS users,<br>&gt;&nbsp; &gt; &gt;<br>&gt;&nbsp; &gt; &gt; I reproduced the results of a protein-membrane system by using force field<br>&gt; GROMOSE87. This protein forms ion channel in membrane.<br>&gt;&nbsp; &gt; &gt; Now if I wanna study the ion conduction through this channel using force<br>&gt; field CHARMM27 in umbrella sampling method, is it possible? Can I use the<br>&gt; results of the system simulation which has been derived by GROMOS87?<br>&gt;&nbsp; &gt;<br>&gt;&nbsp; &gt; By definition, switching to a different forcefield like that usually requires<br>&gt;&nbsp; &gt; the
 regeneration of the system's topology, so your new system
 will be<br>&gt;&nbsp; &gt; different from your old one anyway. In addition, you may need to rename the<br>&gt;&nbsp; &gt; atoms in the coordinate files obtained from previous gromos runs to match<br>&gt;&nbsp; &gt; those in the charmm27 residue files.<br>&gt;&nbsp; &gt;<br>&gt;&nbsp; &gt; --<br>&gt;&nbsp; &gt; ==================================================================<br>&gt;&nbsp; &gt; Peter C. Lai | University of Alabama-Birmingham<br>&gt;&nbsp; &gt; Programmer/Analyst | KAUL 752A<br>&gt;&nbsp; &gt; Genetics, Div. of Research | 705 South 20th Street<br>&gt;&nbsp; &gt; <a rel="nofollow" ymailto="mailto:pcl@uab.edu" target="_blank" href="mailto:pcl@uab.edu">pcl@uab.edu</a> &lt;mailto:<a rel="nofollow" ymailto="mailto:pcl@uab.edu" target="_blank" href="mailto:pcl@uab.edu">pcl@uab.edu</a>&gt; | Birmingham AL 35294-4461<br>&gt;&nbsp; &gt; (205) 690-0808 |<br>&gt;&nbsp; &gt;
 ==================================================================<br>&gt;&nbsp; &gt;<br>&gt;&nbsp; &gt; --<br>&gt;&nbsp; &gt; 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> &lt;mailto:<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>&gt;<br>&gt;&nbsp; &gt; http://lists.gromacs.org/mailman/listinfo/gmx-users<br>&gt;&nbsp; &gt; Please search the archive at<br>&gt; <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>&gt;&nbsp; &gt; Please don't post (un)subscribe requests to the list. Use the<br>&gt;&nbsp; &gt; 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>&gt; &lt;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>&gt;.<br>&gt;&nbsp; &gt; Can't post? Read
 http://www.gromacs.org/Support/Mailing_Lists<br>&gt;<br>&gt;&nbsp; &gt; --<br>&gt;&nbsp; &gt; 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> &lt;mailto:<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>&gt;<br>&gt;&nbsp; &gt; <a rel="nofollow" target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>&gt;&nbsp; &gt; Please search the archive at<br>&gt; <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>&gt;&nbsp; &gt; Please don't post (un)subscribe requests to the list. Use the<br>&gt;&nbsp; &gt; 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>&gt;
 &lt;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>&gt;.<br>&gt;&nbsp; &gt; 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>&gt;<br>&gt;<br>&gt; --<br>&gt; ==================================================================<br>&gt; Peter C. Lai | University of Alabama-Birmingham<br>&gt; Programmer/Analyst | KAUL 752A<br>&gt; Genetics, Div. of Research | 705 South 20th Street<br>&gt; <a rel="nofollow" ymailto="mailto:pcl@uab.edu" target="_blank" href="mailto:pcl@uab.edu">pcl@uab.edu</a> &lt;mailto:<a rel="nofollow" ymailto="mailto:pcl@uab.edu" target="_blank" href="mailto:pcl@uab.edu">pcl@uab.edu</a>&gt; | Birmingham AL 35294-4461<br>&gt; (205) 690-0808 |<br>&gt;
 ==================================================================<br>&gt;<br>&gt; --<br>&gt; 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> &lt;mailto:<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>&gt;<br>&gt; <a rel="nofollow" target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>&gt; 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>&gt; before posting!<br>&gt; Please don't post (un)subscribe requests to the list. Use the<br>&gt; 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>&gt; &lt;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>&gt;.<br>&gt; 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>&gt;<br>&gt;<br>&gt;<br>&gt;<br>&gt;<br>&gt;<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> 
 </div></div></div><br><br> </div> </div>  </div></body></html>