AMBER Archive (2006)

Subject: Re: AMBER: ntt=1 in simulated annealing

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Wed Nov 15 2006 - 01:09:15 CST

Dear Tanya,

the problems could have been appeared because you don't have reference
temperature temp0 in your input. Though I'm not sure that it is the
source of the problems you've got.

Sergey

Tanya Johannsen wrote:
> I tried gamma_ln=1.0 and my simulated annealing run
> didn't work at all--but I doubt that the gamma_ln is
> the culprit. For some reason the &wt section was
> completely ignored and the temperature simply rose to
> 300 K and stayed there. I compared my input file to
> the Nudged Elastic Band simulated annealing tutorial
> which uses ntt=3 and I can't find meaningful
> differences. If anyone could take a look at my input
> file and tell me what I did wrong to make the &wt
> section ignored I would be really grateful. Here it
> is:
>
> This simulated annealing run heats the system to 700 K
> over the course of 5 ps,
> leaves it there for 5 ps, and then cools over a period
> of 90 ps. It uses a Langevin temperature scaling
> rather than Berendsen.
> &cntrl
> imin=0,
> nmropt=1,
> ntx=1,
> irest=0,
> ntpr=200,
> ntwx=500,
> ntf=2,
> ntb=1,
> cut=8,
> ipol=0,
> ntr=1,
> restraint_wt=10,
> restraintmask=':1-382,2293-2674',
> nstlim=200000,
> dt=0.0005,
> ntt=3,
> tempi=0,
> gamma_ln=1.0,
> ntc=2,
> /
> &wt type='TEMP0', istep1=0, istep2=10000, value1=0.0,
> value2=700.0,/
> &wt type='TEMP0', istep1=10001, istep2=20000,
> value1=700.0, value2=700.0,/
> &wt type='TEMP0', istep1=20001, istep2=30000,
> value1=700.0, value2=665.0,/
> &wt type='TEMP0', istep1=30001, istep2=40000,
> value1=665.0, value2=630.0,/
> &wt type='TEMP0', istep1=40001, istep2=50000,
> value1=630.0, value2=595.0,/
> &wt type='TEMP0', istep1=50001, istep2=60000,
> value1=595.0, value2=560.0,/
> &wt type='TEMP0', istep1=60001, istep2=70000,
> value1=560.0, value2=525.0,/
> &wt type='TEMP0', istep1=70001, istep2=80000,
> value1=525.0, value2=490.0,/
> &wt type='TEMP0', istep1=80001, istep2=90000,
> value1=490.0, value2=455.0,/
> &wt type='TEMP0', istep1=90001, istep2=100000,
> value1=455.0, value2=420.0,/
> &wt type='TEMP0', istep1=100001, istep2=110000,
> value1=420.0, value2=385.0,/
> &wt type='TEMP0', istep1=110001, istep2=120000,
> value1=385.0, value2=350.0,/
> &wt type='TEMP0', istep1=120001, istep2=130000,
> value1=350.0, value2=315.0,/
> &wt type='TEMP0', istep1=130001, istep2=140000,
> value1=315.0, value2=280.0,/
> &wt type='TEMP0', istep1=140001, istep2=150000,
> value1=280.0, value2=245.0,/
> &wt type='TEMP0', istep1=150001, istep2=160000,
> value1=245.0, value2=210.0,/
> &wt type='TEMP0', istep1=160001, istep2=170000,
> value1=210.0, value2=175.0,/
> &wt type='TEMP0', istep1=170001, istep2=180000,
> value1=175.0, value2=125.0,/
> &wt type='TEMP0', istep1=180001, istep2=200000,
> value1=125.0, value2=0.0,/
> &wt type='END'/
>
>
>
>
> Thanks,
> Tanya
>
>
> --- Steven Winfield <saw44_at_cam.ac.uk> wrote:
>
>
>> This may or may not be helpful:
>>
>> JChemPhys 120(24) 11432-11441 (2004)
>>
>> This paper states that the optimum gamma is found by
>> integrating the
>> memory function of an NVE simulation of your system,
>> but as a rule of
>> thumb the thermostat frequency (= 2*pi / gamma)
>> should be "a few tens of
>> times smaller than the smallest characteristic
>> frequency of the system
>> to be studied"
>>
>> Steve.
>>
>> Ross Walker wrote:
>>
>>> Hi Tanya,
>>>
>>> The use of such a high gamma_ln in that tutorial
>>>
>> has nothing to do with
>>
>>> the high temperatures it is a function of the way
>>>
>> nudged elastic band
>>
>>> simulations work and the tutorial is specific to
>>>
>> this method.
>>
>>>
>>> For a regular MD simulation you should not use
>>>
>> such a high value of
>>
>>> gamma_ln. I suspect a value of 1.0 should be
>>>
>> perfectly good for your
>>
>>> simulated annealing. You could perhaps set it a
>>>
>> bit higher if you find
>>
>>> that the system is taking too long to reach the
>>>
>> target temperature but
>>
>>> if all is working fine this is probably okay. One
>>>
>> could perhaps argue
>>
>>> that at higher temperatures the number of
>>>
>> collisions that would be
>>
>>> occuring per ps would be higher and so a higher
>>>
>> value of gamma_ln might
>>
>>> be appropriate but I have no idea of the
>>>
>> magnitudes of the changes here.
>>
>>>
>>> Perhaps others can comment some more.
>>>
>>> All the best
>>> Ross
>>>
>>> /\
>>> \/
>>> |\oss Walker
>>>
>>> | HPC Consultant and Staff Scientist |
>>> | San Diego Supercomputer Center |
>>> | Tel: +1 858 822 0854 | EMail:-
>>>
>> ross_at_rosswalker.co.uk |
>>
>>> | http://www.rosswalker.co.uk
>>>
>> <http://www.rosswalker.co.uk/> | PGP Key
>>
>>> available on request |
>>>
>>> Note: Electronic Mail is not secure, has no
>>>
>> guarantee of delivery, may
>>
>>> not be read every day, and should not be used for
>>>
>> urgent or sensitive
>>
>>> issues.
>>>
>>>
>>>
>>>
>>>
> ------------------------------------------------------------------------
>
>>> *From:* owner-amber_at_scripps.edu
>>>
>> [mailto:owner-amber_at_scripps.edu] *On
>>
>>> Behalf Of *Tanya Johannsen
>>> *Sent:* Friday, November 03, 2006 16:39
>>> *To:* amber_at_scripps.edu
>>> *Subject:* Re: AMBER: ntt=1 in simulated
>>>
>> annealing
>>
>>> Thank you for your reply. One question: does
>>>
>> the use of ntt=3 for
>>
>>> simulated annealing (and hence high
>>>
>> temperatures) affect how I
>>
>>> should define gamma_ln? Based on tutorials and
>>>
>> the literature that
>>
>>> I've looked at I thought that gamma_ln=1.0 was
>>>
>> a pretty reasonable
>>
>>> choice for room temperature simulations.
>>>
>> However, in the only
>>
>>> tutorial that I've been able to find that uses
>>>
>> ntt=3 for simulated
>>
>>> annealing
>>>
>>>
> (http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_seven/section5.htm),
>
>>> gamma_ln is equal to 1000.0. Does this have
>>>
>> something to do with the
>>
>>> high temperatures? I have consulted the
>>>
>> literature and it is not
>>
>>> clear to me how gamma_ln should be affected
>>>
>> (if at all) by
>>
>>> performing simulated annealing
>>> rather than a room temperature simulation. I
>>>
>> would be very grateful
>>
>>> if anyone could offer their suggestions on
>>>
>> defining gamma_ln.
>>
>>>
>>> Thank you in advance.
>>>
>>> Tanya
>>>
>>>
>>> */Carlos Simmerling <carlos_at_csb.sunysb.edu>/*
>>>
>> wrote:
>>
>>> you can use the weight changes to make
>>>
>> gradual changes to TEMP0
>>
>>> and it will work fine. Check page 106 of
>>>
>> the Amber9 manual and it
>>
>>> shows you how to do weight changes.
>>>
>>> Tanya Johannsen wrote:
>>>
>>> > Dear AMBER community:
>>> >
>>> > I am working on a simulated annealing
>>>
>> run. My understanding
>>
>>> was that
>>> > ntt=1 is traditionally used for
>>>
>> simulated annealing since it is
>>
>>> > possible to use the tautp parameter to
>>>
>> induce slow and gradual
>>
>>> > temperature changes. However, I saw that
>>>
>> in the AMBER 9 manual
>>
>>> it says
>>> > "Unless you are sure you know what you
>>>
>> are doing, please don't
>>
>>> use
>>> > ntt=1!" If not using ntt=1, what is the
>>>
>> best method to use in
>>
>>> > simulated annealing? My understanding is
>>>
>> that ntt=3 leads to a
>>
>>> > relatively quick adjustment to the
>>>
>> target temperature, so even
>>
>>> if I
>>> > included many small adjustments in
>>>
>> TEMP0, I'm concerned that
>>
>>> it would
>>> > be impossible to create a smooth
>>>
>> temperature curve. I would
>>
>>> appreciate
>>> > any advice on the best choice for "ntt"
>>>
>> in simulated annealing
>>
>>> runs.
>>> >
>>> > Thank you in advance for any
>>>
>> suggestions.
>>
>>> >
>>> > Tanya
>>> >
>>> >
>>>
>>>
> ------------------------------------------------------------------------
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