AMBER Archive (2009)

Subject: Re: [AMBER] temperature rises with igb=1

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Mar 17 2009 - 11:58:05 CDT

it may be useful to NOT restrain the hydrogens, depending on how you
built the initial structure.

On Tue, Mar 17, 2009 at 12:53 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> Hi Bala,
>
>> *3.in*
>>  &cntrl
>>
>> imin=0,ntx=1,irest=0,ntpr=100,ntwr=500,ntwx=500,nstlim=20000,dt=0.001,temp
>> i=100.0,temp0=300.0,
>> tautp=0.5,
>>
>> ntt=3,gamma_ln=1.0,cut=12,ntc=2,ntf=2,tol=0.000001,ntr=1,restraint_wt=25,r
>> estraintmask=':1-22',
>>   ntb=0,igb=1,intdiel=1,extdiel=80,saltcon=0.1,gbsa=1,rgbmax=15
>> /
>
> tautp will be ignored when ntt=3. A restraint_wt of 25 is pretty high for
> MD. Something like 5 would probably be better. If your initial structure is
> strained you might find that a lot of potential energy is quickly dumped
> into the springs as kinetic energy which might take a while to equilibrate
> out.
>
> You also don't say how many atoms you have here. The less atoms you have the
> more noise there will be on the kinetic energy and thus temperature.
>
> Cut=12 is probably way too small for GB and is leading to a net heating of
> your system that the thermostat doesn't keep up with. Hence your temperature
> is always above the target temperature. Ideally with GB you should not use a
> cut off - set cut=999.0, or at the very least make it 18.0 or more. Although
> from the *'s in your output below I think you have more immediate problems
> than just the cut off.
>
>> *5.out*
>>       A V E R A G E S   O V E R  100000 S T E P S
>>  NSTEP =   100000   TIME(PS) =     220.000  TEMP(K) =   340.17  PRESS =
>> 0.0
>
>> *6.out*      A V E R A G E S   O V E R  100000 S T E P S
>>  NSTEP =   100000   TIME(PS) =     320.000  TEMP(K) =*********  PRESS =
>> 0.0
>>  Etot   =  NaN            EKtot   =   3568123.6676  EPtot      =  NaN
>>  BOND   =    851450.1246  ANGLE   =     15111.5468  DIHED      =
>> 1984.8352
>>  1-4 NB =      1179.4403  1-4 EEL =     -2064.5821  VDWAALS    =
>> 155.2364
>>  EELEC  =       404.5486  EGB     =  NaN            RESTRAINT  =
>> 639525195.9927
>>  ESURF=        28.9927
>>  EAMBER (non-restraint)  =  NaN
>
> Your system has blown up. This can be from a combination of things although
> often occurs because your starting structure was highly strained. The tough
> restraints you used were probably sufficient to hold it together but as you
> relaxed them the strained system just flew apart. I suggest you very
> carefully look at the trajectory files produced and see if you can see what
> causes the system to blow up. Note your bond energy in 6.out above is VERY
> high. You can also try running with ntwx=1 or 5 or so this will allow you to
> watch how things blow up. I suspect the problem started to occur from the
> very beginning so you should look carefully there. Also rerun step 6 with
> ntwx=1 and watch what happens.
>
> Good luck,
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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>
>
>
>
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