From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Apr 17 2015 - 17:54:37 CDT
I misremembered. Coordnum works, alpha doesn't. You've patched that
already back in the end of January, and I convolved the two since alpha
depends on coordnum internally. My mistake!
-Josh
On 04/17/2015 05:48 PM, Giacomo Fiorin wrote:
> Hey Josh, what's broken exactly?
>
> NAMD_2.10_Linux-x86_64-multicore with a coordnum variable and a moving
> harmonic restraint works fine.
>
> Giacomo
>
> On Fri, Apr 17, 2015 at 6:43 PM, Josh Vermaas <vermaas2_at_illinois.edu
> <mailto:vermaas2_at_illinois.edu>> wrote:
>
> Hi Chola,
>
> The way I like doing this is to use the collective variables
> module to do umbrella sampling along some reaction coordinate that
> describes the binding process (usually based on coordnum, but
> unfortunately its broken in the released binaries of 2.10).
> Usually this doesn't deform the protein like an SMD pull would,
> since the weakest contacts would break first, and the protein is
> free to do what it wants, so long as the coordination number
> between the two parts is restrained.
>
> -Josh
>
>
> On 04/17/2015 05:26 PM, Chola Regmi wrote:
>> Dear all,
>> I used SMD simulation to calculate the PMF between two protein
>> domains. I oriented the domains
>> along the z-axis and applied the force in one domains using
>> backbone atoms and kept other domain fixed at its COM of backbone
>> atoms using "fixedAtoms on" command. I found the PMF very high as
>> compare to experimental value. When I observed the trajectories I
>> found that not all system of protein uniformly moved along z but
>> the weak interaction region of protein moves faster than strong
>> keeping COM motion correct with structural deformation. For me
>> this gave the information about weak and strong binding sites but
>> not the true PMF. I used spring constant 15 kcal/mol/A^2 and
>> pulling velocity 1A/ns. Can anyone suggest the best way to
>> calculate PMF between protein protein domains using NAMD.
>>
>> Following is the extra-parameter section I used in NVT ensemble.
>>
>> #####################################################
>> fixedAtoms on
>> fixedAtomsFile ref.pdb
>> fixedAtomsCol B
>> #######################################################
>> SMD on
>> SMDFile ref.pdb
>> SMDk 15
>> SMDVel 0.000002 ;#velocity/2fs
>> SMDDir 0 0 -1 ;#pulling direction -z
>> SMDOutputFreq 50
>> ##########################################################
>>
>> Thank you.
>>
>> Chola Regmi
>> Virginia Tech
>
>
>
>
> --
> Giacomo Fiorin
> Assistant Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213
> https://icms.cst.temple.edu/members.html
> http://giacomofiorin.github.io/
>
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