[gmx-users] Re: forward and reverse free energy not consistant (Li Qiang)

[Diana Lousa]

Hello,

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.

Thanks

Diana Lousa
Instituto de Tecnologia Química e Biológica
Universidade Nova de Lisboa
Av. da República – EAN,
2780-157 Oeiras
PORTUGAL


---------- Forwarded message ----------
From: Justin A. Lemkul <jalemkul at vt.edu>
Date: 2008/6/16
Subject: Re: [gmx-users] Re: forward and reverse free energy not
consistant (Li  Qiang)
To: Discussion list for GROMACS users <gmx-users at gromacs.org>


Which GMX version are you using?  There's a known bug in version 3.3.1
that has been fixed in 3.3.3.

-Justin

friendli wrote:
>
> Hi,
>
> I use thermodynamics integration. The protocol is 1000step energy
minimization, 20 ps bond-constraint MD, and then 200ps MD for collecting
dgdl.
>
> thanks
>
> Qiang
>
> Gerrit Groenhof wrote:
>>
>> Looks like hysteresis. Do you do slow growth, or discrete FEP?
>>
>> Gerrit
>>
>>
>>
>>> Dear all Gmxers,
>>>
>>> I am calculating a mutation free energy from L<->A for a five AA
peptides using G96 53a6 force field.
>>> however, my dG_for and dG_rev is quite different.
>>> dG_for(lambda=0.00) = - 9.9 kJ/mol
>>> dG_rev(lambda=1.00) =   1.33 kJ/mol
>>>
>>> Is there anything wrong with setting up topologies?
>>>
>>> Here is the [atoms] part for morphed atoms. and I attached the full .top
in the attachment.
>>> For L->A:
>>> [ atoms ]
>>>    17        CH2      2    LEU     CB      6          0     14.027
 CH3   0   15.035; qtot 1
>>>    18        CH1      2    LEU     CG      7          0     13.019
 DUM   0   13.019; qtot 1
>>>    19        CH3      2    LEU    CD1      7          0     15.035
 DUM   0   15.035; qtot 1
>>>    20        CH3      2    LEU    CD2      7          0     15.035
 DUM   0   15.035; qtot 1
>>>
>>>
>>> For A->L :
>>> [ atoms ]
>>>    17        CH3      2    ALA     CB      6          0     15.035
 CH2    0    14.027; qtot 1
>>>    60        DUM      6    DUM    DUM     24          0    13.019
 CH1    0    13.019
>>>    61        DUM      6    DUM    DUM     24          0    15.035
 CH3    0    15.035
>>>    62        DUM      6    DUM    DUM     24          0    15.035
 CH3    0    15.035
>>>
>>> thanks for help
>>>
>>> LQ
>>> -------------- next part --------------
>>> A non-text attachment was scrubbed...
>>> Name: topol_A2L.top
>>> Type: application/x-extension-top
>>> Size: 15230 bytes
>>> Desc: not available
>>> Url :
http://www.gromacs.org/pipermail/gmx-users/attachments/20080616/562fa99f/topol_A2L.bin
>>> -------------- next part --------------
>>> A non-text attachment was scrubbed...
>>> Name: topol_L2A.top
>>> Type: application/x-extension-top
>>> Size: 15189 bytes
>>> Desc: not available
>>> Url :
http://www.gromacs.org/pipermail/gmx-users/attachments/20080616/562fa99f/topol_L2A.bin
>>>
>>> ------------------------------
>>>
>>> _______________________________________________
>>> gmx-users mailing list
>>> gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
posting!
>>>
>>> End of gmx-users Digest, Vol 50, Issue 50
>>> *****************************************
>>>
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
posting!
>> Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>

--
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080616/9925eb18/attachment.html>