Re: Steered MD along detected routes

From: Johny Telecaster (johnytelecaster_at_gmail.com)
Date: Sat Nov 16 2013 - 10:48:42 CST

sorry,

I'm looking for script for calculation work on time (or position
displacement) dependence. I have not found in the sMD output calculated
work (which should be force*displacement but I not sure n correct units
here) amount done on each sMD step.

Johny

2013/11/16 Johny Telecaster <johnytelecaster_at_gmail.com>

> sorry,
>
> I'm looking for script for calculation
>
>
>
> 2013/11/16 Johny Telecaster <johnytelecaster_at_gmail.com>
>
>> Dear Munir,
>>
>> You investigations are very interesting. From your paper I've understood
>> that to simulate unbinding is easily that binding (what you've actually do
>> in your study) But your approach of multi-point MD might be still very
>> useful.
>>
>>
>> Little example
>>
>> -0.178 1.511 2.406 are the started coordinates corresponded to the COM
>> of my ligand
>>
>> Supposing that I chose from the predicted dissociation path 4 extra
>> points corresponded to the turn regions
>>
>> [-1.443, 2.706, 4.485],
>> [0.180, 1.187, 9.484],
>> [0.402, -2.330, 11.8940],
>> [-0.127, -4.221, 17.162]
>>
>>
>> Here you can see that 5 points (included starting points) are ranged
>> mainly on Z (increasing Z from protein interior to the surrounding)
>>
>> No as I understtod 5 directions could not be defined in one conf file so
>> I should to make 5 subsequent sMD simulations in each of which
>>
>> SMD on
>> SMDFile smd_ref.pdb # corresponded to the ligand positioned in the
>> initial COM xyz
>> SMDk 5
>> SMDVel .00001 ;# 10 A/ns = .01 A/ps = .00001 A/fs
>> SMDDir -1.443, 2.706, 4.485 # corresponded to the 1rst point taken from
>> the pathway
>> SMDOutputFreq 100
>>
>> than the second conf should be
>>
>> SMD on
>> SMDFile smd_ref2.pdb # should be taken as the output from the previous
>> run
>> SMDk 5
>> SMDVel .00001 ;# 10 A/ns = .01 A/ps = .00001 A/fs
>> SMDDir 0.180, 1.187, 9.484 # corresponded to the 2nd point taken from the
>> pathway
>> SMDOutputFreq 100
>>
>> etc (overall 5 simulations).
>>
>> Does such method correct in general ?
>>
>> My suggestion: I suppose that some problems might be arisen during the
>> PMF calculations where ~10 windows extracted from the concatenated
>> trajectory (from those 5 trajectories) will be needed. For example how I
>> specify colvar precisely (typical its position restrictions on Z) for each
>> window?
>>
>> Also could some one provide me with the script for analysis of the sMD
>> data ( I'd like to measure force along time coordinate (not position as in
>> the tutorial).
>>
>> Many thanks for suggestions,
>>
>>
>> Johny
>>
>>
>> 2013/11/16 Munir S. Skaf <skaf_at_iqm.unicamp.br>
>>
>>
>>> Dear Johny,
>>>
>>> Perhaps you don't need to define your SMD routes precisely along a cuved
>>> path, but it may
>>> turn out that a few (say, 3 or 4) turning points on a given pathway are
>>> sufficient to smoothly
>>> drive your ligand out of the enzyme.
>>> You have to make educated guesses to define the turning points.
>>> Please take a look at Leandro Martínez's work:
>>>
>>> J. Phys. Chem. B 2008, 112, 10741–10751
>>> This multi-point SMD approach preserves the desired physics of the
>>> force profile.
>>> Best,
>>> munir
>>>
>>>
>>>
>>> On Sat, Nov 16, 2013 at 9:10 AM, Johny Telecaster <
>>> johnytelecaster_at_gmail.com> wrote:
>>>
>>>> Dear NAMD Developers,
>>>>
>>>>
>>>> I have some questions about stereed MD. In particular I'd like to
>>>> simulate ligand unbinding from the enzyme. Using CAVER Pymol plugin I've
>>>> detected 3 possible paths inside my protein. Now I'd like to run stereed MD
>>>> along each of that routes to measure forces affected on the ligand during
>>>> its motions along each of it. How I could define force directions
>>>> presicely along CAVER paths? Does it possible to define this pathes as the
>>>> colvar restrictions? Please provide me with example.
>>>>
>>>>
>>>> Many thanks for the suggestions,
>>>>
>>>>
>>>> Johny T.
>>>> Scanned and tagged with DSPAM 3.10.2 by Instituto de Quimica - Unicamp
>>>> !DSPAM:106,5287537b107521489016123!
>>>
>>>
>>>
>>>
>>> --
>>> Munir S. Skaf
>>> Institute of Chemistry - Cx. P. 6154
>>> State University of Campinas - UNICAMP
>>> Campinas - SP 13084-862, Brazil
>>> Tel. 55 19 3521 3093 / Fax: 3521 3023
>>>
>>
>>
>

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