Re: Re: puzzle of SMD in NAMD-2.9 and pull code in Gromacs

From: dbaogen (dbaogen_at_gmail.com)
Date: Tue Dec 10 2013 - 20:27:15 CST

Dear Axel,

         Thanks for your reply. Using SMD in NAMD, Amber forece field (ff10) was used. And for pull code in Gromacs, Amber force field(ff03) was used in the published article. The force field parameter for ligand is identical. In addition, the force constant and pulling velocity are the same. Other parameters in simulation, such as temperature(310K), temperature control method (V-rescale), timestep (2fs) are also identical. the configuration file using SMD in NAMD is as following:

coordinates ./1s77_10nsbox.pdb

set temperature 310
set outputname md_4ns

firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
amber yes
parmfile ./1s77_10nsbox.top
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 0.833333333
cutoff 12.0
switching off
pairlistdist 14.0

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
rescaleFreq 50
rescaleTemp $temperature

# Periodic Boundary Conditions
cellBasisVector1 109.0 0. 0.0
cellBasisVector2 0.0 105.0 0.0
cellBasisVector3 0.0 0 103.0
cellOrigin 57.73 54.57 53.63

wrapAll on
margin 2

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0

# Constant Volume Control---NVT
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

# Output
outputName $outputname
restartfreq 1000 ;# 500steps = every 1ps
dcdfreq 1000
xstFreq 1000
outputEnergies 1000
outputPressure 1000

#############################################################
## EXTRA PARAMETERS ##
#############################################################
tclForces on
tclForcesScript fix3gpull1g_wu.tcl

#############################################################
## EXECUTION SCRIPT ##
#############################################################
run 2000000 ;# 4ns

       In my opinion, the protein's rotation and transition are present while pulling a ligand out from its active site due to the interaction between them. But in Gromacs software, the protein itself is nearly kept in a position which can not be moved along with the ligand using pull code. I can not understand it clearly. Thank you for your great help.

Best
Duan Baogen


From: Axel Kohlmeyer
Date: 2013-12-10 22:22
To: dbaogen
CC: namd-l
Subject: Re: namd-l: puzzle of SMD in NAMD-2.9 and pull code in Gromacs
On Tue, Dec 10, 2013 at 1:02 PM, dbaogen <dbaogen_at_gmail.com> wrote:
> Dear all,
>
> Recently, I have a problem in using SMD to pull a ligand out
> from the protein active site. In the course of pulling, the protein is
> moving along with ligand. So the results are not consistent with our
> expectation. If we impose the harmonic restraint on protein, the ligand can
> be pulled out. But the artificial effect would be introduced if we did it
> like that. Would anyone like to give me some suggestions about the SMD
> simulation in NAMD?
>
> In addition, it is found that the pull code in Gromacs can also do
> the SMD simulation. From the published results using pull code in Gromacs,
> the protein itself was not restricted while pulling a ligand out from the
> protien's active site. Would you like to explain the difference between SMD
> in NAMD and pull code in Gromacs? Thanks in advance!

well, first *you* have to explain what were the differences in the
*rest* of the simulation. did you employ the exact same force field,
for example?

axel.



>
> Best
>
> Duan Baogen



--
Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

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