From: ipsita basu (ibasu788_at_gmail.com)
Date: Thu Jul 12 2012 - 01:17:53 CDT
Thank you very much sir for your reply.
I actually want to select the COM of a segment of protein that's why I
choose all the atoms in that segment.
By 400 MD steps I wanted to mean the timestep during which the
z-distance will reduce by the width value. And I will correct it
according to your suggestion.
And I didn't want an isotropic distance, I just want to set the
variable as z distance between the selected group 1 and group2.
And sir you said that this is an input of steered MD, I didn't find a
seperate script for umbrella sampling in the NAMD tutorial. Is there
anything else?
Thank you again.
On 7/11/12, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> Ipsita,
>
> First, your variable involves several thousand atoms. Do you really
> need so many? This could slow down the calculation dramatically. Try
> to express the same quantity using a smaller number of atoms (e.g.
> picking just one atom per molecule or per residue).
>
> Your input describes a form of steered MD calculation, and an
> extremely fast one: the restraint will move all the way in only 400 MD
> timesteps. Maybe you intended to do slower steering, or maybe you
> wanted to split the transition into 400 stages? See targetNumStages in
> the documentation for details.
>
> Your variable describes an isotropic distance. Did you want to look at
> a z projection instead? If yes, see the distanceZ component in the
> doc.
>
> Finally, unlike in "traditional SMD", you don't need position
> restraints because the variable is an internal coordinate of the
> system. It is independent of global translations.
>
> Best,
> Jerome
>
>
> On 11 July 2012 13:48, ipsita basu <ibasu788_at_gmail.com> wrote:
>> Sir,
>> I want to umbrella sampling in my membrane protein simulation to
>> calculate potential mean force. My colvar configuration file is:
>> colvarsTrajFrequency 200
>> colvar {
>> name length
>> distance {
>> group1 {
>> atomNumbersRange 94313-98031
>> }
>> group2 {
>> atomNumbers 1503 2307 2709
>> }
>> }
>> }
>> harmonic {
>> name lenpot
>> colvars length
>> centers 17.0
>> forceConstant 1.0
>> targetCenters 80.0
>> targetNumSteps 400
>> }
>>
>> I want to vary the z-distance between group 1 and group 2.
>> I put the initial zav value of group 1 in centers (centers 17.0)
>> and the zav value of group in targetCenters.
>> Now I am just a beginner in umbrella sampling and I've some queries
>> about this. My questions are:
>> 1. Is that right what I'm doing or I misunderstood?
>> 2. What should be the value of targetNumsteps? Is it should be the
>> value during which the distance will reduce by the given width?
>> 3. should the rest system will be position restrained?
>>
>> Any type of help will be really appreciated.
>> If the questions are bizarre then I'm sorry.
>>
>> Thanking you,
>> Yours faithfully
>> Ipsita
>> --
>> 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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