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From: Ross Walker <ross.rosswalker.co.uk>

Date: Thu, 29 Nov 2007 08:02:24 -0800

*>From page 94 of the amber 9 manual:
*

The time step (psec). Recommended MAXIMUM is .002 if SHAKE is used, or .001

if it isn’t. Note that for temperatures above 300K, the step size should be

reduced since greater temperatures mean increased velocities and longer

distance traveled between each force evaluation, which can lead to

anomalously high energies and system blowup. Default 0.001.

If you don't know what the concept of a timestep is then you need to go to

the library and get yourself some books on molecular simulation and the

concept of integrating Newton's equations of motion.

Note in terms of affect for a system at equilibrium running a shorter

timestep will give you better integration of the equations of motion and in

theory a more 'precise' trajectory. In practice below some threshold one

typically does not see much of a difference - at least over a few ps or so.

2fs is probably bleeding edge for shake simulations, 1.5fs can be better in

some cases, less than this is probably just overkill and uses more cpu time

for a given simulation length. Without shake you need 1.0fs or less. For

highly strained systems, or bad initial structures (such as from homology

modelling) you may need to run initial relaxation runs with a shorter time

step until the system relaxes away from the initial bad state.

Good luck.

Ross

_____

From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of

Denis Courtier

Sent: Thursday, November 29, 2007 05:33

To: amber.scripps.edu

Subject: Re: AMBER: vlimit exceeded, polarizable force field

I have decrease dt value. I am running at two values. One as dt=0.0002 and

another as dt=0.001. Both are running.

Does anybody know how dt affects to my calculation? Thank you.

Denis.

On Nov 29, 2007 11:43 AM, Denis Courtier <amber982.gmail.com> wrote:

Hello everybody.

I am trying to run a polarizable force field, ff02pol.r1.

But, I got an error. Now, it is in md step. The error in my output file is:

vlimit exceeded for step 5; vmax = 36.3511

vlimit exceeded for step 6; vmax = **********

Coordinate resetting (SHAKE) cannot be accomplished,

deviation is too large

NITER, NIT, LL, I and J are : 0 0 9 8 9

Note: This is usually a symptom of some deeper

problem with the energetics of the system.

My input files, for minimization and md, are:

Initial min-n

&cntrl

ipol=1

imin=1, maxcyc=2500, ncyc=1000,

cut=8.0, ntb=1,ntc=2,ntf=2

/

and

300K constant temp MD

&cntrl

ipol=1

imin=0, ntb=1

cut=8.0, ntc=2, ntf=2,

tempi=300.0, temp0=300.0,

ntt=3, gamma_ln=1.0,

nstlim=520000, dt=0.002,

ntpr=50, ntwx=50,

/

Can anybody help me? How can i control vlimit? Where is the origin of my

problem? Does i have to change the ensemble?

Thank you in advance.

Denis.

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Date: Thu, 29 Nov 2007 08:02:24 -0800

The time step (psec). Recommended MAXIMUM is .002 if SHAKE is used, or .001

if it isn’t. Note that for temperatures above 300K, the step size should be

reduced since greater temperatures mean increased velocities and longer

distance traveled between each force evaluation, which can lead to

anomalously high energies and system blowup. Default 0.001.

If you don't know what the concept of a timestep is then you need to go to

the library and get yourself some books on molecular simulation and the

concept of integrating Newton's equations of motion.

Note in terms of affect for a system at equilibrium running a shorter

timestep will give you better integration of the equations of motion and in

theory a more 'precise' trajectory. In practice below some threshold one

typically does not see much of a difference - at least over a few ps or so.

2fs is probably bleeding edge for shake simulations, 1.5fs can be better in

some cases, less than this is probably just overkill and uses more cpu time

for a given simulation length. Without shake you need 1.0fs or less. For

highly strained systems, or bad initial structures (such as from homology

modelling) you may need to run initial relaxation runs with a shorter time

step until the system relaxes away from the initial bad state.

Good luck.

Ross

_____

From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of

Denis Courtier

Sent: Thursday, November 29, 2007 05:33

To: amber.scripps.edu

Subject: Re: AMBER: vlimit exceeded, polarizable force field

I have decrease dt value. I am running at two values. One as dt=0.0002 and

another as dt=0.001. Both are running.

Does anybody know how dt affects to my calculation? Thank you.

Denis.

On Nov 29, 2007 11:43 AM, Denis Courtier <amber982.gmail.com> wrote:

Hello everybody.

I am trying to run a polarizable force field, ff02pol.r1.

But, I got an error. Now, it is in md step. The error in my output file is:

vlimit exceeded for step 5; vmax = 36.3511

vlimit exceeded for step 6; vmax = **********

Coordinate resetting (SHAKE) cannot be accomplished,

deviation is too large

NITER, NIT, LL, I and J are : 0 0 9 8 9

Note: This is usually a symptom of some deeper

problem with the energetics of the system.

My input files, for minimization and md, are:

Initial min-n

&cntrl

ipol=1

imin=1, maxcyc=2500, ncyc=1000,

cut=8.0, ntb=1,ntc=2,ntf=2

/

and

300K constant temp MD

&cntrl

ipol=1

imin=0, ntb=1

cut=8.0, ntc=2, ntf=2,

tempi=300.0, temp0=300.0,

ntt=3, gamma_ln=1.0,

nstlim=520000, dt=0.002,

ntpr=50, ntwx=50,

/

Can anybody help me? How can i control vlimit? Where is the origin of my

problem? Does i have to change the ensemble?

Thank you in advance.

Denis.

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Sun Dec 02 2007 - 06:07:20 PST

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