AMBER Archive (2008)

Subject: Re: AMBER: Compilation of amber8 patched with ramd

From: Vlad Cojocaru (
Date: Tue Jun 24 2008 - 10:07:03 CDT

Dear Francesco ,

Below is a summary of the bugfixes that interfere with the RAMD patch.
We are studying the problem but for now we can only recommend compiling
AMBER8 with the RAMD patch without these bug fixes. I know this is not
ideal. Maybe you should also compile the AMBER8 without the MKL
libraries since anyhow you'll use it just for the RAMD runs.

As for porting RAMD to Amber 10. We definitely consider it. For now, the
limiting factor is my lack of experience with Fortran and parallel

Good Luck,

-------------------------------------------------SUMMARY RAMD and AMBER8
BUGFIXES (message from our
The following patches are towards force.f, sander.f and runmd.f and
might interfere with the ramd patch:

bugfix.33 <>: The forces
for "cap" water are not accompanied by a corresponding energy term.
/(See also bugfixes 40, 43 and 45, below

/bugfix.7 <>: Using a
restraintmask or a bellymask that invokes distance comparisons will fail.
bugfix.13 <>: Several
fixes to sander.QMMM
bugfix.47 <>: Fixes MPI
calls in /sander/ when the /noBTREE/ is set during compilation.
bugfix.52 <>: Manual
setting of /lastrst/ needs to be allowed for regular Ewald simulations.

bugfix.25 <>: Langevin
dynamics will fail when the target temperature is changed during the run.
bugfix.32 <>: The /mden/
file can contain a bad value for pressure when the pressure is not being
bugfix.54 <>: The /ntt=2/
option in sander can result in average temperatures that are too high.
bugfix.56 <>: Update to
bugfix.54, which failed to work properly in parallel.

Some of the above might still be possible to patch together with the
ramd patch. But this i did not test.

I would recommend to only select the patches from the bugfixes page that
are needed. If one of the above bugfixes are needed, we need to have a
look at the differences in the patches?

Francesco Pietra wrote:
> I am trying to compile (serial) amber8 - patched with contributed
> software RAMD - on a UMA type dual opetron machine, Debian Linux lenny
> amd64.
> The RAMD patch, which only modifies sander
> (, has to be applied before any
> bugfix is applied to amber8 (although, perhaps, bugfix not related to
> sander might have been applied; not tried; I just tried bugfix.all and
> it prevented the RAMD patch to be applied)
> Now
> $ ./configure ifort
> AMBERHOME set to /usr/local/amber8
> Setting up for architecture ifort
> MKL_HOME is set to /opt/intel/mkl/
> Using MKL libraries from /opt/intel/mkl/
> Using parallel communication library: none
> config.h created successfully
> $ make serial
> gave error:
> ifort -o addles addspace.o readprm.o readcrd.o
> writcerd.o pick.o rline.o nxt.o intgr.o find.o of.o geti.o unit.o
> getc.o alert.o echo.o get4c.o getd.o wlesprm.o lesprm.o les2prm.o
> checksz.o ../lib/random.o ../lib/mexit.o ../lib/nxtsec.o
> -L/opt/intel/mkl/ -lvml -lmkl_lapack64 -lmkl -lguide
> -lpthread
> ld: skipping incompatible
> /opt/intel/mkl/ when searching for
> ld: cannot find libmkl_intel,so. Actually this is present where it was
> searched. Thus incompatibility?
> serial error 2
> Is it known (or imaginable) if the the problem is raised by having
> patched sander with ramd, or these mkl libraries (which I used for
> both amber10 and dock6.2) are too new for amber8 (not bugfixed)
> anyway? In the first case I could try by commenting out MKL_HOME in my
> .bashrc.
> I am in contact with the German group for RAMD, too. However,
> presently there is no one capable of adapting RAMD to current times.
> It is clear that my only interest with amber8 if to have it running
> patched with RAMD. Otherwise I have both amber10 and amber9 installed.
> In a way, my question is a jump into the past.
> Thanks
> francesco pietra
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Dr. Vlad Cojocaru

EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg

Tel: ++49-6221-533266 Fax: ++49-6221-533298


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