Hi Keith,
I'm not sure if this was addressed in a bugfix or not, but my copy of
AMBER 10 pmemd does ig = -1 for everything. Maybe it could also be a
compiler-related issue? (I used pathscale to compile AMBER 10.)
Anyway, here is a Langevin (NVT) run in pmemd from our cluster:
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 10
| Run on 06/18/2010 at 16:25:44
[-O]verwriting output
File Assignments:
| MDIN: prod_rsvr.in
| MDOUT: ./output/ala3_rsvr.out
| INPCRD: ./rst/ala3_eq.rst
| PARM: ala3.prmtop
| RESTRT: ./rst/ala3_rsvr.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: ./mdcrd/ala3_rsvr.mdcrd
| MDINFO: mdinfo
|LOGFILE: logfile
Here is the input file:
26 ns NVT MD at 400 K
&cntrl
imin = 0, irest = 0, ntx = 1,
iwrap = 1, ntc = 2, ntf = 2,
ntb = 1, cut = 9.0, ntr = 0,
ntt = 3, gamma_ln = 1, ig = -1,
tempi = 400.0, temp0 = 400.0,
nstlim = 13000000, dt = 0.002,
ntpr = 500, ntwx = 500, ntwr = 50000
/
...snip...
Langevin dynamics temperature regulation:
ig = 984168
temp0 = 400.00000, tempi = 400.00000, gamma_ln= 1.00000
Best,
Paul
On Jul 27, 2010, at 7:25 AM, Keith Van Nostrand wrote:
> 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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 27 2010 - 08:00:03 PDT
