[gmx-users] regarding energy run and g_lie

Thu Sep 15 12:04:09 CEST 2011

בתאריך 15 בספטמבר 2011 12:58, מאת גדעון לפידות <glapidoth at gmail.com>:

> Hello GMX users,
>
> I have a couple of questions regrading energy run and g_lie:
> 1. I am interested in calculating the estimated binding energy between pip2
> and a protein using the lie method.
> 2. I have run the protein ligand  complex for 40 ns with counter-ions,
> npt ensemble and PME
> 3. In order to calculate the ligand -sol Eqq and Elj I have run the ligand
> for 10 ns , also adding counter ions.
> 4. The resulting energies from the solvated ligand were around -3000 KJ
> of electrostatic energy and about +200 KJ of lj energy.
>
> So what I am asking is first, is it fair to assume that the positive LJ
> value of the ligand solvent energy is due to the high electrostatics energy
> between ligand and sol?
> And secondly, since the sol-lig elec. energy is much higher than lig-prot
> elec. energy doing simple lie calculation provides a positive binding
> energy, which obviously contradicts the biology. So is the whole calculation
> not valid or can I do some tweaking with lie formula (for instance change
> the alpha and beta parameters) to try and reproduce experimental data.
>
> Thanks,
>
> Gideon
>
> and second
>
>
> 2011/9/14 <gmx-users-request at gromacs.org>
>
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>> Today's Topics:
>>
>>   1. Re: installation of FFTW (Mark Abraham)
>>   2. Potential energy problem (madhumita das)
>>   3. Re: Potential energy problem (Mark Abraham)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Wed, 14 Sep 2011 15:28:30 +1000
>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>> Subject: Re: [gmx-users] installation of FFTW
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <4E703B7E.7020409 at anu.edu.au>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> On 14/09/2011 3:24 PM, ITHAYARAJA wrote:
>> >
>> > Hi
>> >
>> > I am working with RHEL 6 beta, I unable to install the FFTW package
>> > while installation I found the following error,
>>
>> There is no error reported in what you have shown.
>>
>> >
>> >
>> > make[3]: Leaving directory `/home/Ithayaraja/Desktop/
>> > fftw-3.3.1-beta1/tools'
>> > make[2]: Leaving directory
>> > `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/tools'
>> > Making all in m4
>> > make[2]: Entering directory
>> `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4'
>> > make[2]: Nothing to be done for `all'.
>> > make[2]: Leaving directory
>> `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/m4'
>> > make[1]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1'
>> >
>> >
>> > can you help me to find out where i did wrong?
>>
>> Not without knowing your configure line, knowing that you have followed
>> the instructions on the GROMACS webpage, seeing what the actual error
>> message was, and knowing why you're trying to use a beta of a version of
>> FFTW that is a few years out of date. :)
>>
>> Mark
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Wed, 14 Sep 2011 12:59:42 +0530
>> From: madhumita das <madhumita.bioinfo at gmail.com>
>> Subject: [gmx-users] Potential energy problem
>> To: gmx-users at gromacs.org
>> Message-ID:
>>        <CAFa+f=G5hjY62-pPD48BS1y0tvtDOMVLC1EJYeS=
>> Y_Yz808MdQ at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi Gromacs users,
>>
>> I am doing the protein lipid system packing step and thus shrinking and
>> minimizing the system alternately but after first minimization rest of all
>> minimization steps show E pot=nan and no minimization step occurs in the
>> em.log file. How to get rid of this problem? Please help.
>>
>>
>> Yours faithfully,
>>
>> Madhumita Das.
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>> ------------------------------
>>
>> Message: 3
>> Date: Wed, 14 Sep 2011 17:48:52 +1000
>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>> Subject: Re: [gmx-users] Potential energy problem
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <4E705C64.1020105 at anu.edu.au>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> On 14/09/2011 5:29 PM, madhumita das wrote:
>> > Hi Gromacs users,
>> >
>> > I am doing the protein lipid system packing step and thus shrinking
>> > and minimizing the system alternately but after first minimization
>> > rest of all minimization steps show E pot=nan and no minimization step
>> > occurs in the em.log file. How to get rid of this problem? Please help.
>>
>> It is likely that your system is
>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>>
>> Mark
>>
>>
>> ------------------------------
>>
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>> End of gmx-users Digest, Vol 89, Issue 83
>> *****************************************
>>
>
>
> --
>
> Gideon Lapidoth,
>
> MS.c candidate
>
> Hemi Gutman Biophysics Lab
>
> Department of Biochemistry & Molecular Biology
>
> George S. Wise Faculty of Life Sciences
>
> Tel Aviv University
>
> Israel 69978
>
> <http://ashtoret.tau.ac.il/>
>
> Tel: (972-3) 640-9824
>
>
>
>

-- 

Gideon Lapidoth,

MS.c candidate

Hemi Gutman Biophysics Lab

Department of Biochemistry & Molecular Biology

George S. Wise Faculty of Life Sciences

Tel Aviv University

Israel 69978

<http://ashtoret.tau.ac.il/>

Tel: (972-3) 640-9824
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