<div class="gmail_quote">Hello,<br><br>I'm having a similar problem, i.e. inconsistency between forward and reverse free energy calculations, in changing the chirality of a dihedral. In my case it is unlikely that there is histeresis, given that I have a long simulation. Could you be more specific about the bug you're referring to, I checked the reported known bugs and didn't find anything that was likely to cause this strange results.<br>
<br>Thanks<br><br>Diana Lousa<br>
Instituto de Tecnologia Química e Biológica<br>
Universidade Nova de Lisboa<br>
Av. da República – EAN,<br>
2780-157 Oeiras<br>
PORTUGAL<br><br><br>---------- Forwarded message ----------<br>
From: Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Date: 2008/6/16<br>
Subject: Re: [gmx-users] Re: forward and reverse free energy not<br>
consistant (Li Qiang)<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
<br>
<br>
Which GMX version are you using? There's a known bug in version 3.3.1<br>
that has been fixed in <a href="http://3.3.3." target="_blank">3.3.3.</a><br>
<br>
-Justin<br>
<br>
friendli wrote:<br>
><br>
> Hi,<br>
><br>
> I use thermodynamics integration. The protocol is 1000step energy minimization, 20 ps bond-constraint MD, and then 200ps MD for collecting dgdl.<br>
><br>
> thanks<br>
><br>
> Qiang<br>
><br>
> Gerrit Groenhof wrote:<br>
>><br>
>> Looks like hysteresis. Do you do slow growth, or discrete FEP?<br>
>><br>
>> Gerrit<br>
>><br>
>><br>
>><br>
>>> Dear all Gmxers,<br>
>>><br>
>>> I am calculating a mutation free energy from L<->A for a five AA peptides using G96 53a6 force field.<br>
>>> however, my dG_for and dG_rev is quite different.<br>
>>> dG_for(lambda=0.00) = - 9.9 kJ/mol<br>
>>> dG_rev(lambda=1.00) = 1.33 kJ/mol<br>
>>><br>
>>> Is there anything wrong with setting up topologies?<br>
>>><br>
>>> Here is the [atoms] part for morphed atoms. and I attached the full .top in the attachment.<br>
>>> For L->A:<br>
>>> [ atoms ]<br>
>>> 17 CH2 2 LEU CB 6 0 14.027 CH3 0 15.035; qtot 1<br>
>>> 18 CH1 2 LEU CG 7 0 13.019 DUM 0 13.019; qtot 1<br>
>>> 19 CH3 2 LEU CD1 7 0 15.035 DUM 0 15.035; qtot 1<br>
>>> 20 CH3 2 LEU CD2 7 0 15.035 DUM 0 15.035; qtot 1<br>
>>><br>
>>><br>
>>> For A->L :<br>
>>> [ atoms ]<br>
>>> 17 CH3 2 ALA CB 6 0 15.035 CH2 0 14.027; qtot 1<br>
>>> 60 DUM 6 DUM DUM 24 0 13.019 CH1 0 13.019<br>
>>> 61 DUM 6 DUM DUM 24 0 15.035 CH3 0 15.035<br>
>>> 62 DUM 6 DUM DUM 24 0 15.035 CH3 0 15.035<br>
>>><br>
>>> thanks for help<br>
>>><br>
>>> LQ<br>
>>> -------------- next part --------------<br>
>>> A non-text attachment was scrubbed...<br>
>>> Name: topol_A2L.top<br>
>>> Type: application/x-extension-top<br>
>>> Size: 15230 bytes<br>
>>> Desc: not available<br>
>>> Url : <a href="http://www.gromacs.org/pipermail/gmx-users/attachments/20080616/562fa99f/topol_A2L.bin" target="_blank">http://www.gromacs.org/pipermail/gmx-users/attachments/20080616/562fa99f/topol_A2L.bin</a><br>
>>> -------------- next part --------------<br>
>>> A non-text attachment was scrubbed...<br>
>>> Name: topol_L2A.top<br>
>>> Type: application/x-extension-top<br>
>>> Size: 15189 bytes<br>
>>> Desc: not available<br>
>>> Url : <a href="http://www.gromacs.org/pipermail/gmx-users/attachments/20080616/562fa99f/topol_L2A.bin" target="_blank">http://www.gromacs.org/pipermail/gmx-users/attachments/20080616/562fa99f/topol_L2A.bin</a><br>
>>><br>
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>>><br>
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<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (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>
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