On 4/4/17 6:21 AM, Matteo Busato wrote:
Goodmorning to everyone,
I'm writing here because I'm trying to perform a calculation about the Enthalpy
of Vaporization of a system with 434 molecules of an ionic liquid. I've already
read all the previous posts in the forum about this subject and it has come
clear to me how to perform the calculation, however I'm having problems with my
.mdp file when trying to perform the NVT equilibration.
I've read that for such calculation cutoffs must be set = 0 and pbc=none,
however with such parameters I'm forced to use cutoff-scheme=group instead of
Verlet, so the first problem is that 'group' is not configured for GPU
acceleration and I can use just 1 MPI rank (which slows the job time a lot). Is
there a way to perform this calculation with Verlet?
The second problem is that if I set rvdw=0, gromacs gives me an error saying that
(obviously), vdw-switch must be < rvdw. How can I solve this issue?
There's nothing to switch; you're using a plain cutoff.
There's no point trying to use a GPU to simulate one molecule. This simulation
should run in a matter of seconds on a single CPU.
-Justin
I'll post the mdp I'm using here. Thank you in advance.
; Run control
integrator = sd ; Langevin dynamics
tinit = 0
dt = 0.001
nsteps = 1000000 ; 1000 ps
nstcomm = 100
; Output control
nstxout = 500
nstvout = 500
nstfout = 0
nstlog = 500
nstenergy = 500
nstxout-compressed = 0
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme = group
nstlist = 0
ns_type = grid
pbc = no
rlist = 0
; Electrostatics
coulombtype = cutoff
rcoulomb = 0
; van der Waals
vdwtype = cutoff
vdw-modifier = potential-switch
rvdw = 0
rvdw-switch =0
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; EWALD/PME/PPPM parameters
pme_order = 6
ewald_rtol = 1e-06
epsilon_surface = 0
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps = system
tau_t = 1.0
ref_t = 298.15
; Pressure coupling is off for NVT
Pcoupl = No
tau_p = 0.5
compressibility = 4.5e-05
ref_p = 1.0
; Generate velocities to start
gen_vel = yes
gen_temp = 300
gen_seed = -1
; options for bonds
constraints = h-bonds ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Do not constrain the starting configuration
continuation = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 12
dispcorr=no
Matteo Busato
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
