Re: performing SMD in Z using colvar module

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Nov 18 2020 - 07:15:22 CST

Hi Geordano,

The shocking news is that Colvars is documented! You can read all about it here:
http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html

Best,
Jérôme

----- On 18 Nov 20, at 0:22, Ropón-Palacios biodano.geo_at_gmail.com wrote:

> Dear Jérôme,
>
> Thanks so much for you response, i have a question more , what is reference
> atoms ? and as add velocity of pulling and as CALCULATE -10 ? This is center of
> más in Z axis of my ligand ?
>
> Thanks
>
>
> Enviado desde mi iPhone
>
>> El 17 nov. 2020, a la(s) 4:50 a. m., Jérôme Hénin <jerome.henin_at_ibpc.fr>
>> escribió:
>>
>> Hi Geordano,
>>
>> Your Colvars Module configuration would look like this:
>>
>> colvar {
>> name z
>> distanceZ {
>> main {
>> atomNumbers ... # The moving group
>> }
>> ref {
>> atomNumbers ... # The reference group
>> }
>> }
>> }
>>
>>
>> harmonic { # Define a moving harmonic restraint
>> colvars z
>>
>> centers -10.0 # go from -10
>> targetCenters 10.0 # to 10 Angstrom
>> targetNumSteps 2000000 # in 2 million MD steps
>> forceConstant 10. # in kcal/mol/A^2
>> }
>>
>>
>> For an easier definition of the variable, eg. picking the correct atoms and
>> checking that the values are what you expect, you can use the Colvars Dashboard
>> in recent alpha versions of VMD.
>>
>> In any publication using Colvars in NAMD, please don't forget to cite both the
>> NAMD paper and the Colvars paper
>> (https://www.tandfonline.com/doi/full/10.1080/00268976.2013.813594).
>>
>> Best,
>> Jerome
>>
>>
>> ----- On 16 Nov 20, at 23:16, Ropón-Palacios G. biodano.geo_at_gmail.com wrote:
>>
>>> Dear NAMD users,
>>>
>>>
>>> I want run SMD simulation for generte windows to umbrella sampling, but
>>> like me making it using colvar module, is anybody can help me with an
>>> example, for favor.
>>>
>>> My sistem is an protein boudend to a ligand.
>>>
>>>
>>> Best for all,
>>>
>>>
> >> Geordano.

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