Re: umbrella sampling

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Aug 22 2012 - 05:02:11 CDT

It is best to have at least one atom per lipid. You could use all
phosphorus atoms, if there are a few hundreds of them, performance
should still be fine.

Jerome

On 22 August 2012 11:46, ipsita basu <ibasu788_at_gmail.com> wrote:
> Thank you sir for your reply, it is little bit clearer to me. From
> different posts and NAMD manual I understand which has to be set in
> centers and target.
> For group2, I want to select all the phospahte group of the membrane
> monolayer, so I have to choose a large no of atoms which may slow down
> the process. So my question is that instead of choosing atoms can I
> set the COM of the above mentioned molecules as :
> dummyAtom ( 00.99, 00.39, -61.89 ) ?
>
> On 8/22/12, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
>> Ipsita,
>>
>> The force constant is somewhat small, so you observe some amount of
>> fluctuation around the target value. Apart from that, everything seems
>> to be in order. That is, assuming that the collective variable
>> actually describes what you want to look at. Speaking of which, the
>> distanceZ function is described in the user's guide in plain English.
>> I can't add anything to that.
>>
>> Best,
>> Jerome
>>
>>
>> On 22 August 2012 08:52, ipsita basu <ibasu788_at_gmail.com> wrote:
>>> Sir,
>>> I want to observe a protein penetration into membrane,that's why I
>>> want to do umbrella sampling simulation. The configuaration file where
>>> the umbrella sampling is enabled is given below:
>>> colvarsTrajFrequency 200
>>> colvar {
>>> width 1.0
>>> name distanceZ
>>> distance {
>>> group1 {
>>> atomNumbers 97280
>>> }
>>> group2 {
>>> atomNumbers 1235
>>> }
>>> }
>>> }
>>> harmonic {
>>> name lenpot
>>> colvars distanceZ
>>> centers 10.0
>>> forceConstant 1.0
>>> targetCenters -10.0
>>> targetNumSteps 2000000
>>> targetNumStages 30
>>> }
>>> where I put the value of z coordinate of 97280th atom in centers
>>> (centers 10.0). And I want to fix the process for the 97280th atom to
>>> reach from 10.0 to -10.0(targetCenters) in 2000000 steps.
>>> Am I doing right thing or not? Please help as the conception is not clear
>>> to me.
>>> And one more thing is that the traj file is look like:
>>> # step distanceZ
>>> 0 7.87607744204158e+01
>>> 200 7.31112828886414e+01
>>> 400 6.71194308765552e+01
>>> 600 6.29314331811324e+01
>>> 800 5.97378222403360e+01
>>> 1000 5.62958276760813e+01
>>>
>>> My question is that what is the meaning of distanceZ, is it the
>>> distance between the two selected atoms? Then by what rule it
>>> decreases, as the decrease is not same.
>>> Any type of suggestions will be really helpful to me. Please help.
>>>
>>> --
>>> Ipsita Basu
>>> Research Fellow
>>> c/o : Dr. Chaitali Mukhopadhyay
>>> Rajabazar Science College
>>> 92 APC Road
>>> Kolkata - 700009
>>>
>>
>
>
> --
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009

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