On 7/17/15 6:34 AM, Daniele Veclani wrote:
I read the manual and also some examples of free energy calculation.
when I do the simulation:
M(vacuo) --> nothing(vacuo)
I leave only intramolecular interactions.
How can I just leave these interactions? I don't find the answer in the
manual.
"couple-intramol = no" does not subject intramolecular interactions to lambda
coupling. But doing this in vacuo is pointless, because then by definition,
nothing changes.
-Justin
Best regards
D.V.
2015-07-17 10:10 GMT+02:00 <hannes.loeff...@stfc.ac.uk>:
I do not know how your top file looks like and what you have done to it.
The setup procedure to create the topolog file would be as for a standard
MD simulation with M. You would make sure that the "QUI" label referes to
the right indexes in your index file and run TI with you preferred
protocol. This simplified setup procedure ensures that you do not have to
modify the topology file in any way esp. not to have to set up an explicit
B state.
I suggest to read all parts relating to couple-* in the manual. This is
scattered over several places in the text.
Cheers,
Hannes.
________________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Daniele
Veclani [danielevecl...@gmail.com]
Sent: 17 July 2015 08:57
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] solvation free energy
Thank you for your answer.
I read the manual. As I understand it, I should be deleted, from .top
file, the
section of non-bonded parameters. It's right?
Of course, after the VdW I'll change the electrostatic transformation.
Best regards
D.V.
2015-07-16 16:55 GMT+02:00 Hannes Loeffler <hannes.loeff...@stfc.ac.uk>:
The couple-* parameters take already care of including the non-bonded
terms internal to your molecule to correctly describe the transfer of M
to vacuum. That's the point of those parameters so that you would not
have to run an additional "correction" in vacuo. See the discussion in
the manual (it's section 5.3 for Gromacs 4.6.x). You would also need to
compute the electrostatic transformation.
On Thu, 16 Jul 2015 16:26:44 +0200
Daniele Veclani <danielevecl...@gmail.com> wrote:
I'm trying to calculate the solvation free energy of a molecule (M).
I have done:
M+water ---> dum+water
Now I have to do:
M(vacuo) --> dum(vacuo)
In this case I have a problem, in fact I find a DG = 0.00000 and
within the .xvg file there are only zeros.
Where is the problem?
I use gromacs 5.0.4 and my .mdp file (for lambda 00) is:
integrator = sd
tinit = 0
dt = 0.002
nsteps = 2500000
comm_mode = angular
nstcomm = 100
nstxout = 500
nstvout = 500
nstfout = 0
nstlog = 500
nstenergy = 500
nstxout-compressed = 0
cutoff-scheme = group
nstlist = 0
ns_type = simple
pbc = no
rlist = 0
coulombtype = cutoff
rcoulomb = 0
epsilon_r = 1
vdwtype = cutoff
rvdw = 0
DispCorr = no
fourierspacing = 0.12
pme_order = 6
ewald_rtol = 1e-06
epsilon_surface = 0
tcoupl = berendsen
tc_grps = system
tau_t = 0.1
ref_t = 300
Pcoupl = no
tau_p = 1.0
compressibility = 4.5e-05
ref_p = 1.0
free_energy = yes
init_lambda_state = 0
delta_lambda = 0
calc_lambda_neighbors = 1
vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70
0.80 0.90 1.00
coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00
bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00
restraint_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00
mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00
temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00
sc-alpha = 0.5
sc-coul = no
sc-power = 1.0
sc-sigma = 0.3
couple-moltype = QUI
couple-lambda0 = vdw
couple-lambda1 = none
couple-intramol = no
nstdhdl = 10
gen_vel = no
constraints = all-bonds ; we only have C-H bonds here
constraint-algorithm = lincs
continuation = no
lincs-order = 12
Best regards
Daniele Veclani.
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Ruth L. Kirschstein NRSA Postdoctoral Fellow
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