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

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Dec 11 2013 - 00:02:26 CST

On Wed, Dec 11, 2013 at 3:27 AM, dbaogen <dbaogen_at_gmail.com> wrote:
> 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

does the "same" velocity mean the 'same number' or 'the same after
converting units'?

axel.

> 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.

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

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