[gmx-users] problems with pressure control when using implicit solvent
Ming Tang
m21.tang at qut.edu.au
Fri Mar 13 02:32:49 CET 2015
Thanks a lot, Justin.
Do you think a cut-off distance of 2 is enough? I have no idea how big should I extend it to, however, I am trying some cases. If you are not too sure, I will update with you after I finish these cases. The implicit solvent algorithm limits the choice of cut-off method (only plain cut-off can be used).
Much appreciated,
Tony
-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Friday, 13 March 2015 10:54 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] problems with pressure control when using implicit solvent
On 3/12/15 8:03 PM, Ming Tang wrote:
> Dear all,
>
> I am doing a modelling which consist of a peptide of 40 residues. I am using Implicit solvent and controlled the pressure. However, the box keeps shrinking until the system collapse if I use PBC.
>
Implicit solvent should be used without PBC and no pressure coupling.
> If I remove PBC, the pressure will always be 0. I guess this is due to the together use of implicit solvent, pressure control and non-PBC condition. Can anyone give me some advices?
>
> Thanks,
> Tony
>
> title = charmm27
> define = -DPOSRES ; position restrain the protein
> ; Run parameters
> integrator = md-vv ; leap-frog integrator
> nsteps = 5000000 ; 2 * 5000000 = 10 ns
> dt = 0.002 ; 2 fs
> ; Output control
> nstxout = 100000 ; save coordinates
> nstvout = 100000 ; save velocities
> nstxtcout = 1000
> nstenergy = 1000 ; save energies
> nstlog = 1000 ; update log file
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist = 10
> ; ns algorithm (simple or grid)
> ns_type = grid
> ; nblist cut-off
> cutoff-scheme = group
> rlist = 1.2
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = cut-off
> rcoulomb-switch = 0.8
> rcoulomb = 1.2
> ; Relative dielectric constant for the medium and the reaction field
> epsilon_r = 2
> epsilon_rf = 0
> ; Method for doing Van der Waals
> vdw-type = cut-off
> ; cut-off lengths
> rvdw-switch = 0.8
> rvdw = 1.2
>
I suspect "standard" cutoffs (especially combined with plain cutoff methods) will produce artifacts. Usually people use longer cutoffs in implicit solvent.
Check this very carefully.
-Justin
> ; SIMULATED ANNEALING
> ; Type of annealing for each temperature group (no/single/periodic)
> annealing = single
> ; Number of time points to use for specifying annealing in each group
> annealing-npoints = 4
> ; List of times at the annealing points for each group
> annealing-time = 0 10 20 30
> ; Temp. at each annealing point, for each group.
> annealing-temp = 10 100 200 300
>
> ; Temperature coupling is on
> tcoupl = nose-hoover ; nose-hoover thermostat
> tc-grps = System ; coupling groups - more accurate
> tau_t = 5 ; time constant, in ps
> ref_t = 300 ; reference temperature, one for each group, in K
>
> pcoupl = MTTK ; Pressure coupling on in NPT
> pcoupltype = isotropic ; uniform scaling of box vectors
> tau_p = 5 ; time constant, in ps
> ref_p = 1.0 ; reference pressure, in bar
> compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
> refcoord_scaling = com
>
>
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
>
> ; Dispersion correction
> DispCorr = EnerPres ; account for cut-off vdW scheme
>
> ; Velocity generation
> gen_vel = no ; Velocity generation is off
>
> ; IMPLICIT SOLVENT ALGORITHM
> implicit-solvent = GBSA
>
> ; GENERALIZED BORN ELECTROSTATICS
> ; Algorithm for calculating Born radii
> gb-algorithm = OBC
> ; Frequency of calculating the Born radii inside rlist
> nstgbradii = 1
> ; Cutoff for Born radii calculation; the contribution from atoms ;
> between rlist and rgbradii is updated every nstlist steps
> rgbradii = 1.2
> ; Dielectric coefficient of the implicit solvent
> gb-epsilon-solvent = 80
> ; Salt concentration in M for Generalized Born models
> gb-saltconc = 0
> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
> gb-obc-alpha = 1
> gb-obc-beta = 0.8
> gb-obc-gamma = 4.85
> gb-dielectric-offset = 0.009
> sa-algorithm = Ace-approximation
> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of
> GBSA ; The value -1 will set default value for Still/HCT/OBC GB-models.
> sa-surface-tension = -1
>
--
==================================================
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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