constant velocity SMD

From: Narender Singh Maan (nsmaan_at_gmail.com)
Date: Fri Jan 26 2007 - 11:11:39 CST

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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.

• Next message: Narender Singh Maan: "constant velocity SMD"
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• Next in thread: Narender Singh Maan: "constant velocity SMD"
• Reply: Narender Singh Maan: "constant velocity SMD"
• Reply: JC Gumbart: "Re: constant velocity SMD"
• Reply: Cesar Luis Avila: "Re: constant velocity SMD"
• Reply: Pawel Weronski: "force field for H2PO4- and HPO4(-2) ions"
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