DispCorr= EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; assign velocities from Maxwell distribution
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KRISHNA KISHORE@IIT-MADRAS
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the start of the simulation. What can be the possible reason for this kind
of a behavior and what can be done to fix it?
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KRISHNA KISHORE@IIT-MADRAS
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NVT/NPT equilibration and production MD run. So, someone please clarify me
what the widely accepted values for these two would be. If at all I should
use* rvdw = 1.4*, then should -d flag in editconf be atleast 1.4 or can it
be less than that in the case of PBC conditions enabled.
--
KRISHNA KI
mkul"
> Subject: Re: [gmx-users] Re: Alcohol Dehydrogenase MD
>simulationReg
> To: Discussion list for GROMACS users
> Message-ID: <4d8e281b.5020...@vt.edu>
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> Please choose a relevant subjec
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>
> Message: 1
> Date: Wed, 23 Mar 2011 11:46:30 +1100
> From: Mark Abraham
> Subject: Re: [gmx-users] Alcohol Dehydrogenase MD simulationReg
> To: Discussion list for GROMACS users
> Message-ID: <4d8942e6.8020...@anu.edu.au>
> Content-Type: t
as
a result of which important sidechain hydrogen bonds are being lost in the
simulation. Is such behaviour expected or is it because of the non quantum
mechanical treatment of the NADPH molecule that these kind of situations
occur? If anyone has some experience please share it.
--
KRISHNA KISHORE
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