On 5/11/17 9:49 AM, Dan Gil wrote:
Thank you Dr. Lemkul,
The simulations ran, but I have some a question about the results.
Is it natural to have a nonzero mass_lambda dH/dL? My intuition was that
the potential energy does not depend on mass, and my thinking was that the
mass contribution should be very small, if not zero.
It should. Maybe it's a convergence issue?
-Justin
Best Regards,
Dan
On Wed, May 3, 2017 at 10:46 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 5/3/17 10:43 AM, Dan Gil wrote:
Hi Dr. Kausar,
If I want the molecule to have all of its nonbonded interactions with the
rest of the system (solvent) at each lambda, don't I want to have vdwq
option ON for both couple-lambda0 and couple-lambda1?
What I am attempting to do is mutate molecule A to molecule B through the
simulation.
Relative free energy calculations are a little bit of a strange beast; you
do need to set the B-state (couple-lambda1) to "none" and the B-state types
and charges are read from [atoms].
-Justin
Best Regards,
Dan
On Wed, May 3, 2017 at 1:04 AM, Tasneem Kausar <tasneemkausa...@gmail.com
wrote:
In the last line of mdp file couple-lambda0 and couple-lambda1 have the
same vdwq variable. It indicates A and B state of system. So grompp is
complaining about the identical states.
You can also see the alchemistry.org for detail information about the
free
energy calculations.
On Wed, May 3, 2017 at 2:14 AM, Dan Gil <dan.gil9...@gmail.com> wrote:
Thank you Dr. Lemkul,
Following your advice, I was able to calculate the solvation free energy
of
two molecules that I am interested in. The results, unfortunately, were
not
what I expected. I want to try an alternative method, that is, the
alchemical thermodynamic integration method.
If I understand this correctly, I should be able to calculate the free
energy difference between two systems A and B as I change the topology
of
the molecule from A to B in small steps.
I wasn't able to find a tutorial online, but I attempted to try the
method
and I obtained this error from grompp:
WARNING 1 [file grompp.mdp, line 43]:
The lambda=0 and lambda=1 states for coupling are identical
I was hoping if you could help me understand what I am missing in my
topology or mdp file.
Topology:
[ moleculetype ]
HEPT 3
[ atoms ]
1 opls_135 1 HEPT CH3 1 -0.180 12.011
opls_961 0.360 12.011
2 opls_136 1 HEPT CH2 2 -0.120 12.011
opls_962 0.240 12.011
3 opls_136 1 HEPT CH2 3 -0.120 12.011
opls_962 0.240 12.011
4 opls_136 1 HEPT CH2 4 -0.120 12.011
opls_962 0.240 12.011
5 opls_136 1 HEPT CH2 5 -0.120 12.011
opls_962 0.240 12.011
6 opls_136 1 HEPT CH2 6 -0.120 12.011
opls_962 0.240 12.011
7 opls_135 1 HEPT CH3 7 -0.180 12.011
opls_961 0.360 12.011
8 opls_140 1 HEPT H 1 0.060 1.008
opls_965 -0.120 18.998
9 opls_140 1 HEPT H 1 0.060 1.008
opls_965 -0.120 18.998
10 opls_140 1 HEPT H 1 0.060 1.008
opls_965 -0.120 18.998
11 opls_140 1 HEPT H 2 0.060 1.008
opls_965 -0.120 18.998
12 opls_140 1 HEPT H 2 0.060 1.008
opls_965 -0.120 18.998
13 opls_140 1 HEPT H 3 0.060 1.008
opls_965 -0.120 18.998
14 opls_140 1 HEPT H 3 0.060 1.008
opls_965 -0.120 18.998
15 opls_140 1 HEPT H 4 0.060 1.008
opls_965 -0.120 18.998
16 opls_140 1 HEPT H 4 0.060 1.008
opls_965 -0.120 18.998
17 opls_140 1 HEPT H 5 0.060 1.008
opls_965 -0.120 18.998
18 opls_140 1 HEPT H 5 0.060 1.008
opls_965 -0.120 18.998
19 opls_140 1 HEPT H 6 0.060 1.008
opls_965 -0.120 18.998
20 opls_140 1 HEPT H 6 0.060 1.008
opls_965 -0.120 18.998
21 opls_140 1 HEPT H 7 0.060 1.008
opls_965 -0.120 18.998
22 opls_140 1 HEPT H 7 0.060 1.008
opls_965 -0.120 18.998
23 opls_140 1 HEPT H 7 0.060 1.008
opls_965 -0.120 18.998
... And so on with the bonds, pairs, angles, and dihedrals directive.
MDP File:
;Integration Method and Parameters
integrator = md
nsteps = 10000
dt = 0.002
nstenergy = 1000
nstlog = 5000
;Output Control
nstxout = 0
nstvout = 0
;Cutoff Schemes
cutoff-scheme = group
rlist = 1.0
vdw-type = cut-off
rvdw = 2.0
;Coulomb interactions
coulombtype = pme
rcoulomb = 1.0
fourierspacing = 0.4
;Constraints
constraints = all-bonds
;Temperature coupling
tcoupl = v-rescale
tc-grps = system
tau-t = 0.1
ref-t = 300
;Pressure coupling
pcoupl = parrinello-rahman
ref-p = 1.01325
compressibility = 4.5e-5
tau-p = 5
;Free energy calculation
free-energy = yes
init-lambda = 0
delta-lambda = 0.00001
couple-moltype = HEPT
couple-lambda0 = vdwq
couple-lambda1 = vdwq
On Mon, Apr 3, 2017 at 2:05 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 4/3/17 2:01 PM, Dan Gil wrote:
Thank you Dr. Lemkul,
I am trying to run grompp with the md integrator, but I am getting
this
error:
"For proper sampling of the (nearly) decoupled state, stochastic
dynamics
should be used"
Should I ignore this warning with the -maxwarn option and try running
it?
I
will see if I obtain comparable values for ethanol.
People have already done such a comparison and that's why grompp is
telling you this - it's better to use the Langevin integrator. You'll
get
better sampling, particularly towards the end states. Using -maxwarn
tells
grompp "you're trying to prevent me from making a mistake, but I want
to
do
it anyway" :) You'd better have a really, really good reason to try to
override it.
-Justin
Best Regards,
Dan
On Mon, Mar 27, 2017 at 12:51 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 3/26/17 9:40 PM, Dan Gil wrote:
Hi,
I am following Dr. Sander Pronk's and Dr. Justin Lemkul's tutorial
on
calculating free energy of solvation. Is it possible and
theoretically
sound to use the md integrator instead of the sd integrator for
these
calculations?
Langevin dynamics gives better sampling so it is frequently used for
free
energy calculations. You may get comparable results with the
leap-frog
integrator, but I haven never done a side-by-side comparison.
-Justin
I have already done a considerable amount of work using md
integration,
and
I want to make sure that the free energy values I calculate are
consistent
with my previous work.
If using the md integrator is not sound, is there an alternative way
of
calculating solvation energy that will be consistent?
Best Regards,
Dan
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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
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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
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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
jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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