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From: Fabrício Bracht <fabracht1.gmail.com>

Date: Wed, 18 Sep 2013 17:02:25 -0300

Hello. I am using amber12 (fully patched) to perform TI calculations. I am

having somoe problems related to the number of processors used for the

calculation. Everytime I choose set -np bigger than 8, the calculation

starts with the warning:

***** Processor 0

***** System must be very inhomogeneous.

***** Readjusting recip sizes.

In this slab, Atoms found: 6266 Allocated: 6094

(this is for a -np 16 calculation)

The simulation seems to continue, regardless of the warning. I found a

thread that deals with a similar problem, but it is not related to TI

calculations. In this thread, the user was advised to change the ntc and

ntf values. The only combination that works for me is ntc = 2 and ntf = 1.

I was wondering if there is an unwritten limitation to the number of

processors that can be used for a ti simulation.

My mdin file for V0 is given below.

&cntrl

imin = 0,

irest = 1,

ntx = 7,

ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0,

cut = 8.0,

ntr = 0,

ntc = 2,

ntf = 1,

temp0 = 298.0,

ntt = 3,

gamma_ln = 1.0,

nstlim = 1000000, dt = 0.002, ntave = 1000,

ntpr = 1000, ntwx = 1000, ntwr = 1000, ntxo = 2,

ig = 10703, ioutfm = 1, iwrap = 1,

icfe = 1, ifsc = 1, clambda = 0.02544,

noshakemask = ':342', scmask = ':342.H2', idecomp = 1, nmropt = 0,

/

Receptor residues

RRES 1 7102

END

Printing

RES 1 342

END

END

Thank you

_______________________________________________

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AMBER.ambermd.org

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

Received on Wed Sep 18 2013 - 13:30:02 PDT

Date: Wed, 18 Sep 2013 17:02:25 -0300

Hello. I am using amber12 (fully patched) to perform TI calculations. I am

having somoe problems related to the number of processors used for the

calculation. Everytime I choose set -np bigger than 8, the calculation

starts with the warning:

***** Processor 0

***** System must be very inhomogeneous.

***** Readjusting recip sizes.

In this slab, Atoms found: 6266 Allocated: 6094

(this is for a -np 16 calculation)

The simulation seems to continue, regardless of the warning. I found a

thread that deals with a similar problem, but it is not related to TI

calculations. In this thread, the user was advised to change the ntc and

ntf values. The only combination that works for me is ntc = 2 and ntf = 1.

I was wondering if there is an unwritten limitation to the number of

processors that can be used for a ti simulation.

My mdin file for V0 is given below.

&cntrl

imin = 0,

irest = 1,

ntx = 7,

ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0,

cut = 8.0,

ntr = 0,

ntc = 2,

ntf = 1,

temp0 = 298.0,

ntt = 3,

gamma_ln = 1.0,

nstlim = 1000000, dt = 0.002, ntave = 1000,

ntpr = 1000, ntwx = 1000, ntwr = 1000, ntxo = 2,

ig = 10703, ioutfm = 1, iwrap = 1,

icfe = 1, ifsc = 1, clambda = 0.02544,

noshakemask = ':342', scmask = ':342.H2', idecomp = 1, nmropt = 0,

/

Receptor residues

RRES 1 7102

END

Printing

RES 1 342

END

END

Thank you

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Wed Sep 18 2013 - 13:30:02 PDT

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