Thank you very much for your suggestion I appreciate your help regarding my
problem.
I have included following information in my md.mdp and nvt.mdp files. And I
got the trajectory files that is nvt.trr, md.trr. and .edr files too. Is it
seems ok or any thing going wrong for the calculation of surface tension.
Furthermore, I have used 1000 water molecule and 500 nonane molecules and
the box size 0.0 0.0 22.0. Now after getting .trr and .edr files I could
not go further in the calculation of interfacial tension between water and
nonane.
Could you please provide appropriate command to go for surface tension.
Is it like this: g_energy -f nvt.edr -s topol.tpr -o energy.xvg or any
thing else?
after getting energy files please provide some idea for getting surface
tension.
Thank you
title = NON WATER NVT equilibration
;define = -DPOSRES ; position restrain the protein
; Run
parameters-
integrator = md ; leap-frog integrator
nsteps = 100 ; 2 * 5 = 100 ps
dt = 0.002 ; 2 fs
;
; Output control
nstfout = 1000
nstxout = 1000 ; save coordinates every 0.2 ps
nstvout = 1000 ; save velocities every 0.2 ps
nstenergy = 1000 ; save energies every 0.2 ps
nstlog = 1000 ; update log file every 0.2 ps
;
; Center of mass removal
comm_mode = angular ; linear Change to angular for no pbc
comm_grps = System
nstcomm = 10; freq of center of mass removal
;
; Bond
parameters
continuation = yes ; 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 = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.5 ; short-range neighborlist cutoff (in nm)
rvdw = 1.5 ; short-range van der Waals cutoff (in nm)
rcoulomb= 1.5
;
;
Electrostatics
vdwtype = cut-off
coulombtype = PME
energygrps = SOL NON
;
; Temperature coupling is
on
tcoupl = nose-hoover ; modified Berendsen thermostat
nh-chain-length = 1
tc-grps = SOL NON ; two coupling groups - more accurate
tau_t = 0.2 0.2 ; time constant, in ps
ref_t = 250 250 ; reference temperature, one for each group, in K
;
; Pressure coupling is
off---
Pcoupl = no ;berendsen Parrinello-Rahman
tau_p = 4
pcoupltype = isotropic ; isotropic anisotropic
compressibility = 4.5e-5 ; six for anisotropic 4.5e-5 4.5e-5 4.5e-5
4.5e-5 4.5e-5 4.5e-5
ref_p = 1.0 ;six for anisotropic 1.0 1.0 1.0 0.0 0.0 0.0
;
; Periodic boundary
conditions
pbc = xyz ; 3-D PBC
periodic_molecules = no
; Dispersion
correction---
DispCorr = no ; account for cut-off vdW scheme
; Velocity
generation
gen_vel = no ; assign velocities from Maxwell distribution
gen_temp = 260 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
On Sun, Feb 1, 2015 at 4:00 AM, David van der Spoel
wrote:
> On 2015-02-01 00:56, Bishnu Acharya wrote:
>
>> Hi, Gromacs user,
>>
>> I am doing the molecular dynamics simulation of NONANE and WATER. I am
>> struggling to find the surface tension I mean inter facial tension between
>> water and nonane. Could you please kindly provide some guide line for it.
>> Furthermore I am using box structure 0.0 0.0 20.0 is it compulsory to
>> create rectangular box? If so, could you please suggest me how to do it?
>>
>> If you want water/nonane all you need to do is create a periodic box
> with an amount of water and an amount of nonane. These will phase separate
> and you will get two interfaces. Once in equilibrium you can extract the
> surface tension from g_energy. Not that you have two interface and have to
> divide the number by two, then check the units as well, IIRC it is in milli
> Newton / meter which is 0.1 cP.
>
>
> Thank you
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> 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-u
