1. *Were all patches applied *
The output of ./configure is as follows:
-------------------------------------------------------------------------------------------------------------
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 13 patches:
update.1, update.2, update.3, update.4, update.5, update.6, update.7,
update.8, update.9, update.10,
update.11, update.12, update.13, update.14, update.15, update.16,
update.17, update.18, update.19, update.20,
update.21, update.22, update.23, update.24
Available Amber 12 patches:
bugfix.1, bugfix.2, bugfix.3, bugfix.4, bugfix.5, bugfix.6, bugfix.7,
bugfix.8, bugfix.9.bz2_, bugfix.10,
bugfix.11, bugfix.12, bugfix.13, bugfix.14, bugfix.15, bugfix.16,
bugfix.17, bugfix.18.bz2, bugfix.19, bugfix.20,
bugfix.21
There are patches available. Do you want to apply them now? [y/n]
(Recommended Y)
-------------------------------------------------------------------------------------------------------------
2. *AMBER Configuration flags:*
For serial : ./configure gnu
For parallel: ./configure -mpi gnu
3. *AMBER executable used*: sander, sander.MPI and pmemd.MPI
4. *Input *file:
*--------------------------------------------------------------------------------------------*
A-DNA 10-mer: 20ps MD with res on DNA
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 10000, dt = 0.002,
ntpr = 250, ntwx = 250, ntwr = 10000
/
Keep DNA fixed with weak restraints
10.0
RES 1 20
END
END
-------------------------------------------------------------------------------------
5.*Is the failure reproducible?*
Yes, using all the executables, we are getting the same results again
and again.
We have tried for another system and the same problem persists.
We also changed *temp0=30.0K* but it still goes to ~4000.0K.
---------------------------------------------------------------------
Indrajit Deb
Kolkata, India.
Mob: +919239202278
On Wed, May 21, 2014 at 7:44 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed May 21 2014 - 08:00:03 PDT
