Sorry, I should have asked for more info up-front.
Were all patches applied (I think Amber12 has 21)? What executable are
you running? What configure flags did you use? What does your input
file look like? Is the failure reproducible?
-Dan
On Wed, May 21, 2014 at 8:07 AM, Indrajit Deb <biky2004indra.gmail.com> wrote:
> Hi Daniel,
>
> The installations were of same patch level as both were carried out within
> 1 hour gap.
>
> Thanks for your reply.
>
> ----indrajit
>
>
>
>
>
> ---------------------------------------------------------------------
> Indrajit Deb
> Kolkata, India.
> Mob: +919239202278
>
>
> On Wed, May 21, 2014 at 7:33 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> Were both Amber installations at the same patch level?
>>
>> -Dan
>>
>> On Wed, May 21, 2014 at 7:55 AM, Indrajit Deb <biky2004indra.gmail.com>
>> wrote:
>> > Dear Amber users,
>> >
>> > I am facing a peculiar problem in running AMBER (Amber12 and
>> AmberTools13).
>> > I have complied AMBER on 21/05/2014 in a machine having 64 bit Ubuntu
>> 12.04
>> > LTS (server edition) with AMD opteron 6200 (16 core). During the NVT
>> > equilibration process *(tem0=300.0K)* in explicit solvent the temp.
>> reaches
>> > to ~4000.0K and it stays tiil the NSLIM.
>> > *Output*
>> >
>> ------------------------------------------------------------------------------
>> > NSTEP = 5000 TIME(PS) = 10.000 *TEMP(K) = 3908.32* PRESS =
>> > 0.0
>> > Etot = 90471.3668 EKtot = 89960.2013 EPtot =
>> > 511.1655
>> > BOND = 674.8848 ANGLE = 1395.6137 DIHED =
>> > 718.0662
>> > 1-4 NB = 243.6672 1-4 EEL = -394.4273 VDWAALS =
>> > 8058.9215
>> > EELEC = -11037.0200 EHBOND = 0.0000 RESTRAINT =
>> > 851.4594
>> > EAMBER (non-restraint) = -340.2939
>> > Ewald error estimate: 0.1491E+00
>> >
>> ------------------------------------------------------------------------------
>> >
>> > Whereas when I recompiled the same AMBER on the same date in another
>> > machine having 64bit Ubuntu 12.04 LTS (Desktop version) with Intel Xeon
>> > E5-2609 (8 core), the same simulation (as mentioned above) goes fine,
>> where
>> > it satisfies the *temp0*.
>> > *Output*
>> >
>> ------------------------------------------------------------------------------
>> > NSTEP = 5000 TIME(PS) = 10.000 *TEMP(K) = 302.91* PRESS =
>> > 0.0
>> > Etot = -30535.4721 EKtot = 6972.1931 EPtot =
>> > -37507.6652
>> > BOND = 163.7116 ANGLE = 320.7394 DIHED =
>> > 466.8314
>> > 1-4 NB = 163.3470 1-4 EEL = -363.6741 VDWAALS =
>> > 4497.9322
>> > EELEC = -42858.9286 EHBOND = 0.0000 RESTRAINT =
>> > 102.3757
>> > EAMBER (non-restraint) = -37610.0410
>> > Ewald error estimate: 0.5023E-04
>> >
>> ------------------------------------------------------------------------------
>> >
>> > Kindly suggest what could be the reason for this and what should be done
>> in
>> > this case if I am also willing to use the first machine (having AMD
>> > opteron)?
>> >
>> >
>> > Looking forward for your reply.
>> >
>> >
>> > ---------------------------------------------------------------------
>> > Indrajit Deb
>> > Kolkata, India.
>> > Mob: +919239202278
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> 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
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed May 21 2014 - 07:30:04 PDT
