[gmx-users] FEP w/ PME inner loops
Erik Lindahl
lindahl at sbc.su.se
Tue Aug 30 09:27:33 CEST 2005
Hi David,
We found a couple of last minute showstoppers/failed tests, so
hopefully later today :-)
Cheers,
Erik
On Aug 29, 2005, at 11:15 PM, David L. Bostick wrote:
>
>
> Thanks Erik!
>
> I'll check it out in a few days!
>
> 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, 29 Aug 2005, Erik Lindahl wrote:
>
>
>> 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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