Hello,
Because of correlation in the data, I had started using ig = -1 as well. I am
doing Langevin dynamics with Amber 10 pmemd, and my output shows ig = -1
everywhere:
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 10
| Run on 07/23/2010 at 11:37:13
[-O]verwriting output
File Assignments:
| MDIN: mdN_product-23-min_iso10.in
| MDOUT: md197_product-23-min_iso10.out
| INPCRD: md196_product-23-min_iso10.restrt
| PARM: product-23-min_iso10.prmtop
| RESTRT: md197_product-23-min_iso10.restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: md197_product-23-min_iso10.mdcrd
| MDINFO: mdinfo
|LOGFILE: logfile
Here is the input file:
1ns MD
&cntrl
iwrap = 1,
ig = -1,
imin = 0, irest = 1, ntx = 5,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 500000, dt = 0.002,
ntpr = 500, ntwx = 500, ntwr = 1000
/
...snip...
Langevin dynamics temperature regulation:
ig = -1
temp0 = 300.00000, tempi = 300.00000, gamma_ln= 1.00000
Could it be that ig = -1 was not implemented in amber10 pmemd for Langevin
dynamics?
Hopefully I can just correct this in the future.
Sincerely,
Keith Van Nostrand
________________________________
From: g t <sketchfoot.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Sun, July 25, 2010 9:30:30 AM
Subject: Re: [AMBER] random number seed - range
Hi! I ran a quick simulation with ig set to -1 and it was as Paul said. I
had overlooked the ig value in the temperature regulation section. user
error. how embarassing!
Thanks very much for your replies. :)
Best regards,
GT
On 25 July 2010 02:11, Paul S. Nerenberg <psn.berkeley.edu> wrote:
> Hi GT,
>
> I'd like to add to what Ross, Bill, and Tom have stated. First, as
> Bill has already said, you may be overlooking the thermostat
> information that is printed out further down in the output. For
> example, here is a pmemd (AMBER 10) run that I recently did using ig =
> -1:
>
> -------------------------------------------------------
> Amber 10 SANDER 2008
> -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 10
>
> | Run on 06/16/2010 at 18:17:23
>
> ---snip---
>
> Here is the input file:
>
> Aax3 + water: 50 ns NPT MD at 300 K, 1 atm
> &cntrl
> imin = 0, irest = 1, ntx = 5,
> iwrap = 1, ntc = 2, ntf = 2,
> ntb = 2, cut = 10.0, ntr = 0,
> ntp = 1, pres0 = 1.0, taup = 5.0,
> ntt = 2, vrand = 1000, ig = -1, temp0 = 300.0,
> nstlim = 25000000, dt = 0.002,
> ntpr = 500, ntwx = 500, ntwr = 5000
> /
>
> ---snip---
>
> Anderson (strong collision) temperature regulation:
> ig = 28163, vrand = 1000
> temp0 = 300.00000, tempi = 0.00000
>
> ---snip---
>
> As you can see from this example, the random seed used for the
> thermostat is printed down in the temperature regulation section of
> the output and *not* up where the input file is displayed. [Side
> note: the above run was conducted using pmemd in AMBER 10, so I can
> verify that pmemd in AMBER 10 *does* support ig = -1, although since
> you (GT) want to do TI, you're assumably using sander instead.]
>
> Finally, as Tom has said, the output using random seed n should be
> sufficiently different from random seed n+1, provided that the random
> number generator is "good". But if you are uncomfortable with that,
> you can always use your shell's built-in random number generator
> (i.e., the $RANDOM variable) to generate a new random number each time
> you create a new mdin file. When I do TI calculations, I first
> execute a shell script that generates all of the relevant mdin files
> at once (basically a customized version of the one given in the TI
> tutorial on the AMBER website) and I use ig=$RANDOM within that
> script. That way I can ensure that the same random seed is
> automatically placed in the mdin files for both the V0 and V1 systems.
>
> Best,
>
> Paul
>
>
> On Jul 24, 2010, at 4:12 PM, Ross Walker wrote:
>
> > Hi GT,
> >
> > Are you using PMEMD or Sander? If I remember correctly pmemd in
> > AMBER 10
> > does not support the use of ig=-1. Only Sander does. PMEMD from
> > AMBER 11
> > supports the use of ig=-1.
> >
> > All the best
> > Ross
> >
> >> -----Original Message-----
> >> From: g t [mailto:sketchfoot.gmail.com]
> >> Sent: Saturday, July 24, 2010 12:46 PM
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] random number seed - range
> >>
> >> Hi!
> >>
> >> Thanks for your quick reply. I checked the outfiles when ig was set
> >> to
> >> -1
> >> and they stated that ig had been set to -1 every instance, instead
> >> of a
> >> random number based upon the current time & date. I'm afraid I no
> >> longer
> >> have those files to post though.
> >>
> >> My version of AMBER is 10 and is running on linux Red Hat Enterprise
> >> Linux
> >> Server release 5.4. I'm afraid I do not know the compiler for sure,
> >> but
> >> suspect they may have used the comercial intel compiler & fortran
> >> options.
> >>
> >> I think the issue is probably due to the TI limitation you speak
> >> off in
> >> the
> >> second paragraph. If I do have to specify the ig value manually, what
> >> do you
> >> think would be an acceptable range?
> >>
> >> Thanks again,
> >> GT
> >>
> >> On 24 July 2010 14:22, case <case.biomaps.rutgers.edu> wrote:
> >>
> >>> On Sat, Jul 24, 2010, g t wrote:
> >>>>
> >>>> I am ruinning a TI calculation. When I set the random number seed
> >> value
> >>> to:
> >>>>
> >>>> ig = -1
> >>>>
> >>>> The number is not set randomly based on the current date & time.
> >>>
> >>> First, what is you evidence that "ig=-1" is not using a different
> >> seed for
> >>> each run? (The seed chosen is printed in the output file). This
> >> sounds
> >>> like
> >>> a bug, but we need to know the version of Amber, the compiler
> >> (+version)
> >>> and
> >>> OS you are using.
> >>>
> >>> Second, note that you generally cannot use "ig=-1" for TI, since the
> >>> integration scheme (which depends on ig for ntt=3) needs to be the
> >> same
> >>> for each of the two groups. So, for TI, you have to manually choose
> >> a
> >>> different seed for each run, and make it the same in the two mdin
> >> files.
> >>>
> >>> ....dac
> >>>
> >>>
> >>> _______________________________________________
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> >>>
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> >
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>
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Received on Tue Jul 27 2010 - 07:30:04 PDT
