Thomas Cheatham wrote:
>> I'm currently trying to run my systems using AMBER, but got a problem
>> when I'm trying to restart the simulation from previous run. What I did
>> is simply copy the restrt file with coordinations and velocities, then
>> restart the job. But when I check the output data in the .mdout file and
>> found the data at the same time point are obviously different from
>> previous run. I'm showing the output data below,
>>
>
>
>> NSTEP = 19100 TIME(PS) = 19.100 TEMP(K) = 310.64 PRESS = 108.3
>> EELEC = -283272.0143 EHBOND = 0.0000 RESTRAINT = 5825.8596
>>
>
> vs.
>
>
>> NSTEP = 100 TIME(PS) = 19.100 TEMP(K) = 2577.07 PRESS = 3038.9
>> EELEC = -268207.1839 EHBOND = 0.0000 RESTRAINT = 595262.3848
>>
> ...
>
>> ntp=2,pres0=1.0,taup=2.5,
>> ntr=1,
>>
>
> Couple of things to notice; temperature jumps, restraint energy is
> extremely high and you are running constant (anisotropic) pressure
> control. This suggests that the reference coordinates have changed and
> this is an artifact of constant pressure simulation. What happens is that
> during constant pressure, the positions of the restraint coordinates are
> also scaled so that after the run is over, the restraint coordinates not
> longer match the refc coordinates. If you restarted with the original
> refc restraint coordinates, you get the behavior shown. Use the restrt as
> the refc coordinates and it should work (although the restraint energy
> will still be different).
>
>
Thanks a lot! Dr. Cheatham. If I run constant (isotropic) pressure
simulation, will the situation be better? My system is a lipid bilayer
system, that's why I select anisotropic constant pressure simulation
previously.
Another question is, if I don't use the original refc restraint
coordinates all the time, but change it every time when restart the
simulation, then the structure of the restraint part of the system might
change too much if I restart the simulation too many times, right? Will
this be a problem? If so, is there any other way that I can make sure
the structure of the restraint part of the system will be maintained all
the time?
Really appreciate any suggestions.
Kefa
>> GRP1
>> 100.0
>> ATOM 1 13609
>>
>
> This restraint energy is extremely high; you could probably reduce this
> value to 20.0 or even 5.0.
>
> See also:
>
> http://archive.ambermd.org/200807/0055.html
>
>
>
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Received on Wed Aug 19 2009 - 22:42:42 PDT
