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From: Franz Waibl <Franz.Waibl.uibk.ac.at>

Date: Mon, 30 Nov 2020 15:34:44 +0100

Dear Amber community,

I am trying to compute the free energy of hydration of a set of small

molecules at different salt concentrations, using TI. I want to use a

2-step transform (i.e., first remove the charges, then the Van der Waals

part).

However, I have problems figuring out how to set up the electrostatic

step in pmemd (CUDA-version, using Amber 20). Currently, my input file

looks like this:

production 10 ns npt run - Berendsen barostat, TI, remove charges

&cntrl

ntx=1, irest=0,

ioutfm=1,

ntb=2, iwrap=1,

ntp=1, barostat=2, pres0=1.0,taup=1.0,

ntc=2, ntf=1,

ntt=3, tempi=300.0, temp0=300.0, gamma_ln=2,

nstlim=5000000, dt=0.002,

ntwr=50000, ntwx=5000,

ntpr=500,

icfe=1, klambda=1, ifsc=0, timask1=':1', timask2=':2', crgmask=':2',

ifmbar=1, mbar_states=11, tishake=0,

mbar_lambda=0.00,0.10,0.20,0.30,0.40,0.50,0.60,0.70,0.80,0.90,1.00,,

clambda=0.50,

/

(Of course, I have equivalent input files for the other lambda values).

Of this run, I am discarding the first 40% (4ns) as equilibration. The

1st and second residue are 2 copies of my molecule (the topology was

created using tleap by "combine { solute solute solvent }".)

The problem is that I am getting very large free energies (e.g, 130

kcal/mol for caffeine, favoring lambda=0). This occurs with and without

the salt, so I think the problem is not related to the ions.

Furthermore, I don't think that convergence is the problem, because I

tried using 10x longer simulations for a few systems, and the results

are very similar.

The VdW contribution is rather close to zero, and therefore doesn't

compensate the high values. I assume that this is realistic, and that

the problem is related to the electrostatics part. (is this correct?)

I would be very thankful for any suggestions on what might be wrong here...

Best regards,

Franz Waibl

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Mon Nov 30 2020 - 07:00:03 PST

Date: Mon, 30 Nov 2020 15:34:44 +0100

Dear Amber community,

I am trying to compute the free energy of hydration of a set of small

molecules at different salt concentrations, using TI. I want to use a

2-step transform (i.e., first remove the charges, then the Van der Waals

part).

However, I have problems figuring out how to set up the electrostatic

step in pmemd (CUDA-version, using Amber 20). Currently, my input file

looks like this:

production 10 ns npt run - Berendsen barostat, TI, remove charges

&cntrl

ntx=1, irest=0,

ioutfm=1,

ntb=2, iwrap=1,

ntp=1, barostat=2, pres0=1.0,taup=1.0,

ntc=2, ntf=1,

ntt=3, tempi=300.0, temp0=300.0, gamma_ln=2,

nstlim=5000000, dt=0.002,

ntwr=50000, ntwx=5000,

ntpr=500,

icfe=1, klambda=1, ifsc=0, timask1=':1', timask2=':2', crgmask=':2',

ifmbar=1, mbar_states=11, tishake=0,

mbar_lambda=0.00,0.10,0.20,0.30,0.40,0.50,0.60,0.70,0.80,0.90,1.00,,

clambda=0.50,

/

(Of course, I have equivalent input files for the other lambda values).

Of this run, I am discarding the first 40% (4ns) as equilibration. The

1st and second residue are 2 copies of my molecule (the topology was

created using tleap by "combine { solute solute solvent }".)

The problem is that I am getting very large free energies (e.g, 130

kcal/mol for caffeine, favoring lambda=0). This occurs with and without

the salt, so I think the problem is not related to the ions.

Furthermore, I don't think that convergence is the problem, because I

tried using 10x longer simulations for a few systems, and the results

are very similar.

The VdW contribution is rather close to zero, and therefore doesn't

compensate the high values. I assume that this is realistic, and that

the problem is related to the electrostatics part. (is this correct?)

I would be very thankful for any suggestions on what might be wrong here...

Best regards,

Franz Waibl

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Mon Nov 30 2020 - 07:00:03 PST

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