From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Mon Jun 19 2017 - 08:43:37 CDT
Hi Francesco,
Thanks for the suggestion.I am looking to study the binding of a peptide
(~30 residues) to a lipid bilayer. The reason why we aren't using something
like ABF is because it is really hard to define a reaction coordinate for
our problem. We also speculate the binding leads to some partial secondary
structure formation. Since aMD has been able to tackle protein folding in
solution, we are thinking about using GaMD for our purpose. What's your
take on this?
On Mon, Jun 19, 2017 at 1:36 AM, Francesco Pietra <chiendarret_at_gmail.com>
wrote:
> Hi Chitrak:
> Just a remark about what I meant with my answer to your question. Should
> you want to have a ligand of a protein moving, rotating etc , in order to
> take its correct position in the BP, which is a common dream, that is not
> what MD (nor its biased form GaMD) can do. The problem of getting the
> lowest free energy in such cases is dealt with by ABF, FEP, and other
> variants of these, and perhaps also by different, less common algorithms.
>
> good look
> chiendarret
>
> On Sun, Jun 18, 2017 at 9:57 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu>
> wrote:
>
>> Thanks Jeevan and David. I was indeed making the mistake of not switching
>> on "accelMD". That solved the problem.
>>
>> Regards,
>> Chitrak.
>>
>> On Sun, Jun 18, 2017 at 12:02 PM, David Hardy <dhardy_at_ks.uiuc.edu> wrote:
>>
>>> Hi Chitrak,
>>>
>>> This looks to me like a syntax problem in your config file.
>>>
>>> If you haven't done so, you also need to specify "accelMD on" in your
>>> config file. Otherwise the accelMDG options will not activate.
>>>
>>> Best regards,
>>> Dave
>>>
>>> --
>>> David J. Hardy, Ph.D.
>>> Theoretical and Computational Biophysics
>>> Beckman Institute, University of Illinois
>>> dhardy_at_ks.uiuc.edu
>>> http://www.ks.uiuc.edu/~dhardy/
>>>
>>>
>>> On Jun 18, 2017, at 9:20 AM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:
>>>
>>> Hi Francesco,
>>>
>>> Thanks for your suggestion, I shall definitely get back to the paper.
>>> However, for now, I am trying to get the GaMD simulation run without an
>>> error. Would you know how to do that? I tried both NAMD 2.12 and the
>>> current nightly build version, both gave the following error in the log file
>>>
>>> Warning: The following variables were set in the
>>> Warning: configuration file but will be ignored:
>>> Warning: accelMDdual (accelMD)
>>> ERROR: The following variables were set in the
>>> ERROR: configuration file but are NOT VALID
>>> ERROR: accelMDsigma0D
>>> ERROR: accelMDSigma0P
>>> ERROR: accelMDGEquiSteps
>>> ERROR: accelMDGEquiPrepSteps
>>> ERROR: accelMDGcMDSteps
>>> ERROR: accelMDGcMDPrepSteps
>>> ERROR: accelMDGRestart
>>> ERROR: accelMDGiE
>>> ERROR: accelMDG
>>>
>>>
>>> On Sun, Jun 18, 2017 at 2:04 AM, Francesco Pietra <chiendarret_at_gmail.com
>>> > wrote:
>>>
>>>> Be careful. Re-read the paper with GaMD implemented in NAMD, cheeking
>>>> whether it could potentailly solve your need, and compare with ABF and FEP
>>>> (about which there is far more experience) before embarking in what could
>>>> well later be disappointing (after huge amount of work)
>>>>
>>>> chiendarret
>>>>
>>>> On Sat, Jun 17, 2017 at 10:16 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu>
>>>> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I was wondering if anyone has worked with GaMD in NAMD 2.12 or the
>>>>> latest nightly build of NAMD. When I try it, all the GaMD options are
>>>>> ignored and the job crashes. Is there any tutorial on how to get this to
>>>>> work?
>>>>>
>>>>>
>>>>> Regards,
>>>>> Chitrak.
>>>>>
>>>>
>>>>
>>>
>>>
>>
>
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