[gmx-users] FEP w/ PME inner loops

[Erik Lindahl]

Hi David,

Try checking out the latest CVS, which has  direct-space interactions  
with correct PME corrections.

Or actually, please hold off until tomorrow since I'm hours away from  
finally releasing the first of two real betas of 3.3!

Cheers,

Erik


On Aug 17, 2005, at 9:03 PM, David L. Bostick wrote:

>
>
> Hello,
>
> I successfully checked out and compiled the CVS code of 2004/11/01,  
> which
> is supposed to include the PME inner loops for free energy  
> calculations.
> HOwever, when I grompp the topology with free_energy=yes, I get the
> following warning:
>
> WARNING 1 [file 15.mdp, line unknown]:
>   You are using lattice sum electrostatics with free energy  
> integration.
>   This might give wrong results, since the lattice contribution to  
> the free
>   energy not calculated.
>
> Was the warning left in the code even though the lattice  
> contribution is
> supposed to be calculated? I would appreciate any advisement. This  
> warning
> does not exist in the current cvs version, even though the inner  
> loops are
> not there.  It is replaced by a note as follows:
>
> NOTE:
>   State B has non-zero total charge: -1.000000e+00
>
> Should I disregard these warnings and notes? I want to be sure all  
> is well
> before I start calculating things.
>
> Thanks in advance,
> David
>
>
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- 
> =-=-=-=-=
> David Bostick                    Office: 262 Venable Hall
> Dept. of Physics and Astronomy            Phone:  (919)962-0165
> Program in Molecular and Cellular Biophysics
> UNC-Chapel Hill
> CB #3255 Phillips Hall                dbostick at physics.unc.edu
> Chapel Hill, NC 27599                       http://www.unc.edu/ 
> ~dbostick
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- 
> =-=-=-=-
>
> On Mon, 8 Aug 2005, David wrote:
>
>
>> On Mon, 2005-08-08 at 12:54 -0400, David L. Bostick wrote:
>>
>>> Hello,
>>>
>>> Berk instructed me awhile ago that the free-energy innerloops  
>>> that allow
>>> for outputting dV/d(lambda) that includes the PME contribution  
>>> can be found
>>> in the CVS code of 2004/11/01.  I would like to check out this  
>>> version of
>>> the code, but I am only familiar with the regular checkout  
>>> procedure of the
>>> latest CVS code as outlined on the web page.  Could someone  
>>> instruct me on
>>> how to check out a version from a specific date? Forgive me if  
>>> instructions
>>> are actually on the web site ... if they are, I somehow missed them.
>>>
>> man cvs says:
>> cvs co -D 2004-11-01 gmx
>>
>>
>>>
>>> Also, given that these innerloops were discontinued in the code,  
>>> there must
>>> have been some problem with them.  Is there any reason for  
>>> caution when
>>> doing FEP with this version? I would be appreciative of any  
>>> advice in using
>>> this code.
>>>
>>
>> Erik will commit the new loops real soon now, but I don't knwo  
>> what was
>> wrong with the old ones.
>>
>>
>>>
>>> Thanks in advance,
>>> David
>>>
>>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- 
>>> =-=-=-=-=-=
>>> David Bostick                    Office: 262 Venable Hall
>>> Dept. of Physics and Astronomy            Phone:  (919)962-0165
>>> Program in Molecular and Cellular Biophysics
>>> UNC-Chapel Hill
>>> CB #3255 Phillips Hall                dbostick at physics.unc.edu
>>> Chapel Hill, NC 27599                       http://www.unc.edu/ 
>>> ~dbostick
>>> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- 
>>> =-=-=-=-=-
>>> _______________________________________________
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>> --
>> David.
>> _____________________________________________________________________ 
>> ___
>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,          75124 Uppsala, Sweden
>> phone:  46 18 471 4205          fax: 46 18 511 755
>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/ 
>> ~spoel
>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
>> +++++
>>
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