<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>Thanks for your kind reply .</span></div><div><span>Sincerely,<br>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 face="Arial" size="2"> <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> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Wednesday, May 2, 2012 7:02 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] GROMOS87 and CHARMM27<br> </font> </div> <br>
<br><br>On 5/2/12 10:30 AM, Shima Arasteh wrote:<br>><br>> Thanks for your reply.<br>><br>> What do you mean by running for some additional time?<br><br>You're introducing a new force field, which includes different representation of <br>atoms and a different potential energy function. You can't just take a <br>configuration generated by Gromos87, apply CHARMM27 parameters to it, and expect <br>continuity in the job. You need to re-equilibrate the structure under the new <br>parameters.<br><br>> I guess,I have to modulate the structure from the first point. Right? I think<br>> the results of last run using gromos is not beneficial at all, because the<br>> parameters are different for sure.<br>><br><br>Having little idea what you're doing, I'll tend to agree.<br><br>-Justin<br><br>> Cheers,<br>> Shima<br>><br>> --------------------------------------------------------------------------------<br>> *From:*
Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Shima Arasteh <<a ymailto="mailto:shima_arasteh2001@yahoo.com" href="mailto:shima_arasteh2001@yahoo.com">shima_arasteh2001@yahoo.com</a>>; Discussion list for GROMACS<br>> users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Wednesday, May 2, 2012 5:34 PM<br>> *Subject:* Re: [gmx-users] GROMOS87 and CHARMM27<br>><br>><br>><br>> On 5/2/12 12:21 AM, Shima Arasteh wrote:<br>> ><br>> > Dear Justin,<br>> > I don't want to compare the forcefields results.<br>> > Yes, Iwant to use some old information in conjunction with something new.<br>> > In fact, I have to regenerate a structure, which has modulated using gmx.ff.<br>> > After it, I am going to study it using
umbrella sampling technique. I want to do<br>> > it using charmm27. I want to know if it is possible? Is it correct that I use<br>> > the results of the job done by gmx? Or I need to repeat the job using charmm?<br>> ><br>><br>> Structures are force field agnostic. You can process them with whatever force<br>> field you like. If the structure you want to simulate with CHARMM was previous<br>> produced by Gromos87 (as I suspect, from looking at the thread below) then you<br>> will definitely need to run for some additional time. The force field is<br>> different and thus you need to re-equilibrate the system (at the very least)<br>> under the new parameters.<br>><br>> -Justin<br>><br>> > Thanks,<br>> > Shima<br>> ><br>> > --------------------------------------------------------------------------------<br>> > *From:* Justin A.
Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> <mailto:<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>><br>> > *To:* Shima Arasteh <<a ymailto="mailto:shima_arasteh2001@yahoo.com" href="mailto:shima_arasteh2001@yahoo.com">shima_arasteh2001@yahoo.com</a><br>> <mailto:<a ymailto="mailto:shima_arasteh2001@yahoo.com" href="mailto:shima_arasteh2001@yahoo.com">shima_arasteh2001@yahoo.com</a>>>; Discussion list for GROMACS<br>> > users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>><br>> > *Sent:* Tuesday, May 1, 2012 9:44 PM<br>> > *Subject:* Re: Fw: [gmx-users] GROMOS87 and CHARMM27<br>> ><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<br>> > 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>>
--------------------------------------------------------------------------------<br>> > > *From:* Peter C. Lai <<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a>> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a><br>> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a>>>><br>> > > *To:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> > <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a
ymailto="mailto:gmx-users@gromacs.org" 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 ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a> <mailto:<a ymailto="mailto:pcl@uab.edu"
href="mailto:pcl@uab.edu">pcl@uab.edu</a>> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a><br>> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a>>> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a>><br>> > <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a>>>>><br>> > > > To: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> > <mailto:<a
ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>><br>> > > <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" 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 ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a>> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a><br>> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a>>> <mailto:<a ymailto="mailto:pcl@uab.edu"
href="mailto:pcl@uab.edu">pcl@uab.edu</a> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a>><br>> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a>>>><br>> > | Birmingham AL 35294-4461<br>> > > > (205) 690-0808 |<br>> > > > ==================================================================<br>> > > ><br>> > > > --<br>> > > > gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>> <mailto:<a ymailto="mailto:gmx-users@gromacs.org"
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==================================================================<br>> > > Peter C. Lai | University of Alabama-Birmingham<br>> > > Programmer/Analyst | KAUL 752A<br>> > > Genetics, Div. of Research | 705 South 20th Street<br>> > > <a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a>> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a>>><br>> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a>> <mailto:<a ymailto="mailto:pcl@uab.edu" href="mailto:pcl@uab.edu">pcl@uab.edu</a><br>> <mailto:<a ymailto="mailto:pcl@uab.edu"
href="mailto:pcl@uab.edu">pcl@uab.edu</a>>>> |<br>> > Birmingham AL 35294-4461<br>> > > (205) 690-0808 |<br>> > > ==================================================================<br>> > ><br>> > > --<br>> > > gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>><br>> > <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a
ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>>><br>> > > <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> > > Please search the archive at<br>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">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 ymailto="mailto:gmx-users-request@gromacs.org"
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href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>>>.<br>> > > Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">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 href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>> ><br>> > ========================================<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 href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><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 href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use
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