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

[Justin Lemkul]

On 2/23/17 9:07 AM, Anurag Dobhal wrote:
> 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

If you don't have solvent, there's no reason to restrain anything.  Normally one 
restrains the solute to allow the solvent to relax around it.  Here, this serves 
no purpose.

> ; 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

Note you also need cutoff-scheme = group here.

> 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

As I said before, you can't use PME (grompp will fail anyway, because you can't 
have PME without PBC).  Use a plain cutoff.

> 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

Dispersion correction is also not applicable.

-Justin

> ; 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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>>
>>
>

-- 
==================================================

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

==================================================