[gmx-users] Potential Energy is positive on minimizing the system

[Anurag Dobhal]

Dear Justin,

I would like to know weather the parameters below are correct for NVT
equilibiration whicle doig a simulation in vaccum ?

define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = simple ; search neighboring grid cells
nstlist = 0 ; 10 fs
rlist = 0.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.0 ; short-range electrostatic cutoff (in nm)
rvdw = 0.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 0 ; cubic interpolation
fourierspacing = 0.0 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Other ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 300 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = no ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed

Thank You




*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Thu, Feb 23, 2017 at 7:23 PM, Anurag Dobhal <
anurag.dobhal at nano-medicine.co.in> wrote:

> Thank you !
>
>
>
>
> *Anurag Dobhal*
> *Graduate Student (Bioprocess Technology)*
> *Institute of Chemical Technology, Mumbai*
> *Contact: +91 8898486877*
>
>
> On Thu, Feb 23, 2017 at 7:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 2/23/17 8:29 AM, Anurag Dobhal wrote:
>>
>>> Thank you. Should I not use PME and PBC while performing simulations in
>>> Vaccum ?
>>>
>>>
>> No, you should not.  Use no PBC and infinite cutoffs (all cutoffs set to
>> zero) to mimic vacuum conditions.  Otherwise you're simulating some type of
>> diffusely occupied crystal environment.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>

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