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From: Fabian gmail <fabian.glaser.gmail.com>

Date: Thu, 3 Dec 2015 14:15:17 +0200

Dear Hannes,

thanks a lot, to be honest it will greatly help you if you go over the input files I prepared for the heating, equil and and prod for one lambda, and let me now what to change…. I just was trying to following the protocol on Kaus et al (dx.doi.org/10.1021/ct400340s | J. Chem. Theory Comput. 2013, 9, 4131−4139) since they do exactly what I want…. but I don't’ have experience at all with TI…. so any suggestion will be more than welcomed.

If you have the time, I would be very grateful if you could take a quick look and tell me what to correct or what is the protocol your recommend in this case. I already reduced the minimisation steps to 500.

So regarding the equilibration time I should increment the time by how much ? I start with 500 ps for lambda 0, then 1 ps lambda 0.1 then 1.5 0.2 etc.? Is that a good strategy?

I paste here the four input files I prepared following Kaus paper (again my goal is to try and calculate solvation energy of a drug). I would be very grateful for any correction….This inputs are for clambda = 0, but I thought to use them for every lambda, now that you mention the void issue, I understand I need to increase the equilibration time.

Here they are, in the order I thought to use it for every lambda, obviously changing the clambda value in each case see PBS file below.

I will highly appreciate also if you could recommend how to make the analysis later, I understand they are several tools….

Thanks!!

Fabian

===========

minimisation 500 steps

&cntrl

imin = 1,

ntmin = 2,

maxcyc = 500,

ntpr = 20,

ntwe = 20,

ntb = 1,

cut = 8.0

clambda = 0.0,

scalpha = 0.5,

scbeta = 12.0,

logdvdl = 0,

icfe = 1,

ifsc = 1,

timask1='',

timask2=':1',

scmask1='',

scmask2=':1',

/

&ewald

/

============

heating constant vol 500 ps

&cntrl

imin = 0,

nstlim = 250000,

irest = 0,

ntx = 1,

dt = 0.002,

nmropt = 1,

ntb=2,

ntp=1,

ntt = 3,

gamma_ln = 2,

pres0 = 1.0,

temp0 = 300.0,

tempi = 0.0,

tautp = 1.0,

cut = 8.0,

ntc = 2,

ntf = 1,

ntxo=2,

ioutfm = 1,

iwrap = 1,

ntwe = 1000,

ntwx = 1000,

ntpr = 1000,

ntwr = 5000,

clambda = 0.0,

scalpha = 0.5,

scbeta = 12.0,

logdvdl = 0,

icfe = 1,

ifsc = 1,

timask1='',

timask2=':1',

scmask1='',

scmask2=':1',

/

&ewald

/

/

&wt TYPE='TEMP0', istep1=0, istep2=25000,

value1=0.1, value2=300.0,

/

&wt TYPE='END'

/

============

heating constant vol 500 ps

&cntrl

imin = 0,

nstlim = 250000,

irest = 0,

ntx = 1,

dt = 0.002,

nmropt = 1,

ntb=2,

ntp=1,

ntt = 3,

gamma_ln = 2,

pres0 = 1.0,

temp0 = 300.0,

tempi = 0.0,

tautp = 1.0,

cut = 8.0,

ntc = 2,

ntf = 1,

ntxo=2,

ioutfm = 1,

iwrap = 1,

ntwe = 1000,

ntwx = 1000,

ntpr = 1000,

ntwr = 5000,

clambda = 0.0,

scalpha = 0.5,

scbeta = 12.0,

logdvdl = 0,

icfe = 1,

ifsc = 1,

timask1='',

timask2=':1',

scmask1='',

scmask2=':1',

/

&ewald

/

/

&wt TYPE='TEMP0', istep1=0, istep2=25000,

value1=0.1, value2=300.0,

/

&wt TYPE='END'

/

============

Constant Volume production 5ns

&cntrl

imin = 0,

nstlim = 2500000,

irest = 1,

ntx = 5,

dt = 0.002,

ntt = 3,

temp0 = 300.0,

gamma_ln = 2.0,

ig = -1,

ntc = 2,

ntf = 1,

ntb=1,

ntp=0,

ntxo=2,

ioutfm = 1,

iwrap = 1,

ntwe = 1000,

ntwx = 10000,

ntpr = 10000,

ntwr = 20000,

icfe = 1,

ifsc = 1,

clambda = 0.0,

scalpha = 0.5,

scbeta = 12.0,

logdvdl = 0,

ifmbar = 1,

bar_intervall = 100,

bar_l_min = 0.0,

bar_l_max = 1.0,

bar_l_incr = 0.1,

timask1='',

timask2=':1',

scmask1='',

scmask2=':1',

/

&ewald

/

================

#!/bin/bash

#PBS -l nodes=1:ppn=8

#PBS -N lam0

cd $PBS_O_WORKDIR

pmemd=/opt/amber14/bin/pmemd.MPI

mpirun="/usr/local/bin/mpirun -np 8"

prmtop="../../prmtop/SKF_avo_solv.prmtop"

inpcrd="../../prmtop/SKF_avo_solv.inpcrd"

echo "Minimising..."

$mpirun $pmemd -i min0.in -p $prmtop -c $inpcrd -O -o min0.out -e min0.en -inf min0.info -r min0.rst -l min0.log

echo "Heating constant pressure 0.5 ns ..."

$mpirun $pmemd -i heat0.in -p $prmtop -c min0.rst -O -o heat0.out -e heat0.en -inf heat0.info -r heat0.rst -x heat0.nc -l heat0.log

echo "Equil constant volume 0.5 ns..."

$mpirun $pmemd -i equil0.in -p $prmtop -c heat0.rst -O -o equil0.out -e equil0.en -inf equil0.info -r equil0.rst -x equil0.nc -l equil0.log

echo "Production constant volume 5 ns..."

$mpirun $pmemd -i prod0.in -p $prmtop -c equil0.rst -O -o prod0.out -e prod0.en -inf prod0.info -r prod0.rst -x prod0.nc -l prod0.log

=====================

Dr. Fabian Glaser

Head of the Structural Bioinformatics section

Bioinformatics Knowledge Unit - BKU

The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering

Technion - Israel Institute of Technology, Haifa 32000, ISRAEL

fglaser at technion dot ac dot il

Tel: +972 4 8293701

http://bku.technion.ac.il

*> On 3 Dec 2015, at 1:46 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk> wrote:
*

*>
*

*> On Wed, 2 Dec 2015 16:49:20 +0200
*

*> Fabian gmail <fabian.glaser.gmail.com <mailto:fabian.glaser.gmail.com>> wrote:
*

*>
*

*>> Dear Jason,
*

*>>
*

*>> Thanks a lot for the detailed explanation, so in the paper I am
*

*>> following, they minimised once, and then use the same minimised
*

*>> molecule (in this case a drug Improving the Efficiency of Free Energy
*

*>> Calculations in the Amber Molecular Dynamics Package Joseph W.
*

*>> Kaus,*,† Levi T. Pierce,†,‡ Ross C. Walker,†,‡ and J. Andrew
*

*>> cCammon†,§,∥,⊥) and then perform IT calculation.
*

*>>
*

*>> So the protocol I will be using will something like this:
*

*>>
*

*>> 0) minimize 20,000 steps ONCE for lambda = 0. 5 and then for each
*

*>> lambda for lambda 0, 0,1, 0,2, etc. … 1 do the following:
*

*>
*

*> That's just overkill. All you want to do with the minimisation step is
*

*> to eliminate close contacts which could lead to high forces in MD and
*

*> thus potential instability. A few hundred steps should be enough.
*

*>
*

*> You could do the same protocol for every lambda as it costs very
*

*> little. Keep in mind that you are extrapolating away from the
*

*> references state and thus "equilibration" of later lambdas
*

*> potentially needs more time. Not sure what the convergence behaviour
*

*> for decoupling is but at the end-point your molecule will have created
*

*> a void and will be filled with water.
*

*>
*

*> You could take over the data from the previous neighbour lambda if you
*

*> wanted to but in practice this means that you would have to run all
*

*> lambdas one after another.
*

*>
*

*>
*

*>> 1) heating to 300 K during 500 ps at constant pressure
*

*>> 2) equilibrate at constant volume during 500 ps
*

*>> 3) production for 5 ns at constant volume x 3
*

*>>
*

*>> This protocol is different than in the A9 tutorial, but sounds more
*

*>> right for my purpose, does it sounds a right protocol? This is to
*

*>> calculate the DG of solvation (disspereance of a drug in water).
*

*>
*

*> With constant volume you will get the Helmholtz free energy, not Gibbs.
*

*>
*

*>
*

*> Cheers,
*

*> Hannes.
*

*>
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
*

*> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
*

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Thu Dec 03 2015 - 04:30:03 PST

Date: Thu, 3 Dec 2015 14:15:17 +0200

Dear Hannes,

thanks a lot, to be honest it will greatly help you if you go over the input files I prepared for the heating, equil and and prod for one lambda, and let me now what to change…. I just was trying to following the protocol on Kaus et al (dx.doi.org/10.1021/ct400340s | J. Chem. Theory Comput. 2013, 9, 4131−4139) since they do exactly what I want…. but I don't’ have experience at all with TI…. so any suggestion will be more than welcomed.

If you have the time, I would be very grateful if you could take a quick look and tell me what to correct or what is the protocol your recommend in this case. I already reduced the minimisation steps to 500.

So regarding the equilibration time I should increment the time by how much ? I start with 500 ps for lambda 0, then 1 ps lambda 0.1 then 1.5 0.2 etc.? Is that a good strategy?

I paste here the four input files I prepared following Kaus paper (again my goal is to try and calculate solvation energy of a drug). I would be very grateful for any correction….This inputs are for clambda = 0, but I thought to use them for every lambda, now that you mention the void issue, I understand I need to increase the equilibration time.

Here they are, in the order I thought to use it for every lambda, obviously changing the clambda value in each case see PBS file below.

I will highly appreciate also if you could recommend how to make the analysis later, I understand they are several tools….

Thanks!!

Fabian

===========

minimisation 500 steps

&cntrl

imin = 1,

ntmin = 2,

maxcyc = 500,

ntpr = 20,

ntwe = 20,

ntb = 1,

cut = 8.0

clambda = 0.0,

scalpha = 0.5,

scbeta = 12.0,

logdvdl = 0,

icfe = 1,

ifsc = 1,

timask1='',

timask2=':1',

scmask1='',

scmask2=':1',

/

&ewald

/

============

heating constant vol 500 ps

&cntrl

imin = 0,

nstlim = 250000,

irest = 0,

ntx = 1,

dt = 0.002,

nmropt = 1,

ntb=2,

ntp=1,

ntt = 3,

gamma_ln = 2,

pres0 = 1.0,

temp0 = 300.0,

tempi = 0.0,

tautp = 1.0,

cut = 8.0,

ntc = 2,

ntf = 1,

ntxo=2,

ioutfm = 1,

iwrap = 1,

ntwe = 1000,

ntwx = 1000,

ntpr = 1000,

ntwr = 5000,

clambda = 0.0,

scalpha = 0.5,

scbeta = 12.0,

logdvdl = 0,

icfe = 1,

ifsc = 1,

timask1='',

timask2=':1',

scmask1='',

scmask2=':1',

/

&ewald

/

/

&wt TYPE='TEMP0', istep1=0, istep2=25000,

value1=0.1, value2=300.0,

/

&wt TYPE='END'

/

============

heating constant vol 500 ps

&cntrl

imin = 0,

nstlim = 250000,

irest = 0,

ntx = 1,

dt = 0.002,

nmropt = 1,

ntb=2,

ntp=1,

ntt = 3,

gamma_ln = 2,

pres0 = 1.0,

temp0 = 300.0,

tempi = 0.0,

tautp = 1.0,

cut = 8.0,

ntc = 2,

ntf = 1,

ntxo=2,

ioutfm = 1,

iwrap = 1,

ntwe = 1000,

ntwx = 1000,

ntpr = 1000,

ntwr = 5000,

clambda = 0.0,

scalpha = 0.5,

scbeta = 12.0,

logdvdl = 0,

icfe = 1,

ifsc = 1,

timask1='',

timask2=':1',

scmask1='',

scmask2=':1',

/

&ewald

/

/

&wt TYPE='TEMP0', istep1=0, istep2=25000,

value1=0.1, value2=300.0,

/

&wt TYPE='END'

/

============

Constant Volume production 5ns

&cntrl

imin = 0,

nstlim = 2500000,

irest = 1,

ntx = 5,

dt = 0.002,

ntt = 3,

temp0 = 300.0,

gamma_ln = 2.0,

ig = -1,

ntc = 2,

ntf = 1,

ntb=1,

ntp=0,

ntxo=2,

ioutfm = 1,

iwrap = 1,

ntwe = 1000,

ntwx = 10000,

ntpr = 10000,

ntwr = 20000,

icfe = 1,

ifsc = 1,

clambda = 0.0,

scalpha = 0.5,

scbeta = 12.0,

logdvdl = 0,

ifmbar = 1,

bar_intervall = 100,

bar_l_min = 0.0,

bar_l_max = 1.0,

bar_l_incr = 0.1,

timask1='',

timask2=':1',

scmask1='',

scmask2=':1',

/

&ewald

/

================

#!/bin/bash

#PBS -l nodes=1:ppn=8

#PBS -N lam0

cd $PBS_O_WORKDIR

pmemd=/opt/amber14/bin/pmemd.MPI

mpirun="/usr/local/bin/mpirun -np 8"

prmtop="../../prmtop/SKF_avo_solv.prmtop"

inpcrd="../../prmtop/SKF_avo_solv.inpcrd"

echo "Minimising..."

$mpirun $pmemd -i min0.in -p $prmtop -c $inpcrd -O -o min0.out -e min0.en -inf min0.info -r min0.rst -l min0.log

echo "Heating constant pressure 0.5 ns ..."

$mpirun $pmemd -i heat0.in -p $prmtop -c min0.rst -O -o heat0.out -e heat0.en -inf heat0.info -r heat0.rst -x heat0.nc -l heat0.log

echo "Equil constant volume 0.5 ns..."

$mpirun $pmemd -i equil0.in -p $prmtop -c heat0.rst -O -o equil0.out -e equil0.en -inf equil0.info -r equil0.rst -x equil0.nc -l equil0.log

echo "Production constant volume 5 ns..."

$mpirun $pmemd -i prod0.in -p $prmtop -c equil0.rst -O -o prod0.out -e prod0.en -inf prod0.info -r prod0.rst -x prod0.nc -l prod0.log

=====================

Dr. Fabian Glaser

Head of the Structural Bioinformatics section

Bioinformatics Knowledge Unit - BKU

The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering

Technion - Israel Institute of Technology, Haifa 32000, ISRAEL

fglaser at technion dot ac dot il

Tel: +972 4 8293701

http://bku.technion.ac.il

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Thu Dec 03 2015 - 04:30:03 PST

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