AMBER Archive (2009)

Subject: Re: [AMBER] problem with cutoff

From: Yunjie Zhao (yjzhao.wh_at_gmail.com)
Date: Mon May 04 2009 - 07:58:00 CDT

Hi Ross,

  Thanks for your reply. I am trying to do molecular simulations
with different cut-offs of EEL / VDW in implicit solvent model. Maybe the
cutoff should be much larger. It seems that the sander can not do this.
  I have tried to install PMEMD. But there is a problem. Can you tell me
what the problem is?

  The input and output are as follows:
$./configure linux_em64t ifort lam
Intel ifort compiler found; version information:
Version 10.1
Use Intel MKL? (better performance) (answer yes or no):
no
File config_data/fft.pubfft being used...
File config_data/linux_em64t.ifort being used...
File config_data/interconnect.lam being used...
configure assumes lam files are in /opt/lammpi.
PMEMD Configurate successfully completed.

$ make install
cd src && make install
make[1]: Entering directory `/export/home/zyj/amber9/src/pmemd/src'
ifort -o pmemd gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o
parallel_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o inpcrd_dat.o
dynamics_dat.o img.o parallel.o pme_direct.o pme_recip.o pme_fft.o fft1d.o
bspline.o pme_force.o pbc.o nb_pairlist.o cit.o dynamics.o bonds.o angles.o
dihedrals.o runmd.o loadbal.o shake.o runmin.o constraints.o axis_optimize.o
gb_ene.o veclib.o gb_force.o timers.o pmemd_lib.o runfiles.o file_io.o
bintraj.o pmemd_clib.o pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o
nmr_lib.o get_cmdline.o master_setup.o alltasks_setup.o pme_setup.o
ene_frc_splines.o nextprmtop_section.o -L/opt/lammpi/lib -llamf77mpi
-lmpi -llam -ldl -lpthread -limf -lsvml
-Wl,-rpath=/opt/lam/gnu/lib:/opt/pgi/linux86-64/7.0-7/libso:/opt/lammpi/lib:/opt/intel/fce/10.1.012/lib
/opt/lammpi/lib/liblam.so: undefined reference to `openpty'
make[1]: *** [pmemd] Error 1
make[1]: Leaving directory `/export/home/zyj/amber9/src/pmemd/src'
make: *** [install] Error 2

 Thanks!

2009/5/4 Ross Walker <ross_at_rosswalker.co.uk>

> Hi Yunjie,
>
> You cannot do this with Sander and I'm not sure why you'd want to. In fact
> I'm not sure why you think an electrostatic cutoff in GB is warrantied at
> all - especially one as small as 9 angstroms...
>
> What do you hope to gain by having a second even smaller vdw cutoff? You
> still need to generate a pair list and loop over atoms so it is unlikely to
> save you much if anything at all. PMEMD supports dual cutoffs for periodic
> boundary simulations, where potentially it can make sense but I do not
> think
> it supports this for GB. You could hack it into egb.f yourself fairly
> easily
> but I don't see why you'd want to do that unless you wanted to experiment
> with EEL / VDW effects as a function of cut off distance.
>
> In my opinion (others may differ here) if you are NOT doing periodic
> boundary simulations with PME (such as GB) then you should NOT use any form
> of cutoff... period!
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> > Behalf Of Yunjie Zhao
> > Sent: Sunday, May 03, 2009 8:53 PM
> > To: AMBER_at_ambermd.org
> > Subject: [AMBER] problem with cutoff
> >
> > Dear Amber users,
> >
> > Using Amber 9, I am trying to do molecular simulations with GB
> > implicit
> > solvent model. I have done a cut-off to distinguish short-range and
> > long-range interactions. Now I am trying to distinguish the vdw and
> > electrostatic interactions, such as cutoff of vdw with 6 angstrom and
> > cutoff of electrostatic with 9 angstrom. How can I do this? Can anyone
> > tell
> > me how to write the input file?
> >
> > My input file:
> > MD Generalised Born simulation
> > &cntrl
> > imin = 0, ntb =0,
> > igb = 1, ntpr = 10000, ntwx = 10000,
> > ntt = 3,gamma_ln = 1.0,
> > tempi = 300.0, temp0 = 300.0,
> > nstlim = 10000000, dt = 0.001,
> > cut = 9
> > /
> >
> > Thanks!
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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