constant velocity SMD

From: Narender Singh Maan (nsmaan_at_gmail.com)
Date: Fri Jan 26 2007 - 11:44:41 CST

>
> Dear Users,
>
> I have some questions about setting up my system (a protein-ligand system
> with constant velocity SMD)…In this i am trying to pull the ligand out of
> the protein. So,
>
> 1) as it says in namd/smd tutorial it keep one atom fixed (beta 1)
> and smd-atom moving (occupancy 1)…but in my situation i just want to pull
> the ligand out of the protein's binding site and do not want to keep
> anything fixed (in protein). So in this situation I have all my beta column
> set to zero. So the question is how do I find out the vector direction?
> (since it requires to find the vector direction that links fixed and smd
> atom, and I don't have the fixed atom!)
>
> 2) I can define a fixed Center of mass of my ligand and make it as
> smd-atom and pull it out from that point but how can I define all the atoms
> (as smd-atoms) of my ligand and pull them out together?..
>
> 3) Many of the related papers that I see for SMD shows the timestep
> of 1fs!!..why is it so??..normally in MD we keep it 2fs…..is it that SMD is
> more stable with 1fs timestep??..
>
>
> This here is my coordinate *xx.pdb* file (segname PRO1 is my protein part
> and segname INH1 is my ligand)
>
> ATOM 3670 HG23 THR 234 -2.295 20.477 -15.764
> 0.00 0.00 PRO1
>
> ATOM 3671 C THR 234 -5.395 20.707 -12.464
> 0.00 0.00 PRO1
>
> ATOM 3672 OT1 THR 234 -6.336 20.719 -13.291
> 0.00 0.00 PRO1
>
> ATOM 3673 OT2 THR 234 -5.441 21.306 -11.370
> 0.00 0.00 PRO1
>
> ATOM 3674 C29 RPR 1 -1.666 -5.800 10.832
> 0.00 0.00 INH1
>
> ATOM 3675 N30 RPR 1 -2.030 -6.192 9.650
> 0.00 0.00 INH1
>
> ATOM 3676 H30 RPR 1 -2.660 -6.969 9.662
> 0.00 0.00 INH1
>
> This here is my smdfile *xx.ref* file
>
> ATOM 3670 HG23 THR 234 -2.295 20.477 -15.764
> 1.00 0.00 PRO1
>
> ATOM 3671 C THR 234 -5.395 20.707 -12.464
> 1.00 0.00 PRO1
>
> ATOM 3672 OT1 THR 234 -6.336 20.719 -13.291
> 1.00 0.00 PRO1
>
> ATOM 3673 OT2 THR 234 -5.441 21.306 -11.370
> 1.00 0.00 PRO1
>
> ATOM 3674 C29 RPR 1 -1.666 -5.800 10.832
> 1.00 0.00 INH1
>
> ATOM 3675 N30 RPR 1 -2.030 -6.192 9.650
> 1.00 0.00 INH1
>
> ATOM 3676 H30 RPR 1 -2.660 -6.969 9.662
> 1.00 0.00 INH1
>
>
>
> And this here is a part of my xx.conf file
>
> ___________________________________________________________________
>
> fixedAtoms on
>
> fixedAtomsFile xx.ref
>
> fixedAtomsCol B (???)
>
> SMD on
>
> SMDfile xx.ref
>
> SMDk 5;# 347.395 pNA
>
> SMDvel 0.00001 ; # 10A/ns since ts is 1fs
>
> SMDDir -0.3534 -0.4135 0.8391 ; # (??just a test)
>
> SMDOutputFreq 100
>
> __________________________________________________________________
>
> Any suggestions would be of great help
>
> Thank you
> singh
>
> P.S. I searched the list for these questions but please pardon me if i
> have missed the already answered related questions.
>
>
>

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