Re: constant velocity SMD

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Fri Jan 26 2007 - 12:34:36 CST

Which SMD tutorial are you following? The one used to stretch a protein?
The idea in that tutorial is to keep one end fixed while pulling from
the other.
I think that for using 2 fs step you should use some rigid bonds
algorithm for hydrogens.
Regards

Narender Singh Maan escribió:
>
> 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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