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From: David Case <case.scripps.edu>

Date: Tue, 26 Apr 2005 20:36:45 -0700

On Tue, Apr 26, 2005, Wu, Xiongwu (NIH/NHLBI) wrote:

*>
*

*> I did Langevin dynamics simulations with an alanine dipeptide molecule
*

to

*> examine the effect of stopping COM motion. A box of 60*60*60 was set to
*

*> avoid the molecule from flying away. With gamma_ln=10/ps, temp0=400K,
*

*> IPS=1, and nstlim=100,000,000, I get the following average temperature:
*

*> nscm(steps) 0 10 30 100
*

*> 300 1000
*

*> Average temperature(K): 399.65 404.67 411.53 421.19
*

*> 425.82 427.51
*

Although at first glance, this seems very weird, I think I understand what

is

going on.

Note that "ndfmin" is set in mdread to reflect the number of degrees of

freedom removed from the system. So, in the table above, ndfmin=0 for

nscm=0,

but ndfmin=6 for the other columns. This affects how the temperature is

calculated, but does not affect the nature of the random forces or the

friction. So, the "real" temperature is lower than that reported by Amber

by

a factor of (3*nat-ndfmin)/(3*nat). If the alanine dipeptide has 22

atoms,

this factor is 0.909, which roughly explains the difference between the

nscm=0

and nscm=1000 values: by 1000 steps, the system has effectively

reequilibrated

to a system with 66 degrees of freedom, but Amber is calculating the

temperature as if there were only 60 degrees of freedom. So, the reported

temperature is wrong, by a noticeable amount. For values of nscm between

0

and 1000, you essentially have a system that is trapped between the two

degrees of freedom.

Note that this is not really a problem with the trajectories: it is a

problem

with how temperature is calculated and reported. All other properties of

the

ensemble should be correct, and the "true" average (internal) temperature

is

probably 400K in all the above examples. Amber is just not calculating

the

temperature correctly, because it does not know how many effective degrees

of

freedom there are.

My prediction (tm) is that if you did something similar for a larger

system,

the temperature differences in these sorts of runs would be much smaller.

But you are correct in one sense: setting nscm>0 with the current version

of

Amber leads to inconsistent results with Langevin dynamics.

Question: does the system actually "fly away" with nscm=0 and long

Langevin

dynamic runs? If not, we should probably not require nscm=0 when Langevin

is selected.

Thanks for running these tests!.....dac

Received on Wed Apr 05 2006 - 23:49:57 PDT

Date: Tue, 26 Apr 2005 20:36:45 -0700

On Tue, Apr 26, 2005, Wu, Xiongwu (NIH/NHLBI) wrote:

to

Although at first glance, this seems very weird, I think I understand what

is

going on.

Note that "ndfmin" is set in mdread to reflect the number of degrees of

freedom removed from the system. So, in the table above, ndfmin=0 for

nscm=0,

but ndfmin=6 for the other columns. This affects how the temperature is

calculated, but does not affect the nature of the random forces or the

friction. So, the "real" temperature is lower than that reported by Amber

by

a factor of (3*nat-ndfmin)/(3*nat). If the alanine dipeptide has 22

atoms,

this factor is 0.909, which roughly explains the difference between the

nscm=0

and nscm=1000 values: by 1000 steps, the system has effectively

reequilibrated

to a system with 66 degrees of freedom, but Amber is calculating the

temperature as if there were only 60 degrees of freedom. So, the reported

temperature is wrong, by a noticeable amount. For values of nscm between

0

and 1000, you essentially have a system that is trapped between the two

degrees of freedom.

Note that this is not really a problem with the trajectories: it is a

problem

with how temperature is calculated and reported. All other properties of

the

ensemble should be correct, and the "true" average (internal) temperature

is

probably 400K in all the above examples. Amber is just not calculating

the

temperature correctly, because it does not know how many effective degrees

of

freedom there are.

My prediction (tm) is that if you did something similar for a larger

system,

the temperature differences in these sorts of runs would be much smaller.

But you are correct in one sense: setting nscm>0 with the current version

of

Amber leads to inconsistent results with Langevin dynamics.

Question: does the system actually "fly away" with nscm=0 and long

Langevin

dynamic runs? If not, we should probably not require nscm=0 when Langevin

is selected.

Thanks for running these tests!.....dac

Received on Wed Apr 05 2006 - 23:49:57 PDT

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