AMBER Archive (2004)

Subject: Re: AMBER: LES question

From: Lishan Yao (yaolisha_at_mail.msu.edu)
Date: Thu Feb 12 2004 - 07:59:02 CST

I tested both versions. They work fine.
I clean all the binary files and recompile amber. Now everything is
fine. sander.LES can run well.

Lishan

On Wed, 2004-02-11 at 15:03, Carlos Simmerling wrote:
> that seems like a different problem than
> the one you had before, since this looks related to mpi,
> not to LES. maybe it is a network problem?
>
> you might also try testing this without mpi first.
> that's always a good idea when you have trouble.
> carlos
>
> ----- Original Message -----
> From: "Lishan Yao" <yaolisha_at_mail.msu.edu>
> To: <amber_at_scripps.edu>
> Sent: Wednesday, February 11, 2004 2:52 PM
> Subject: Re: AMBER: LES question
>
>
> > It still can't be done correctly. This is the error message.
> > p0_3901: (26.572858) net_send: could not write to fd=5, errno = 14
> > p0_3901: p4_error: net_send write: -1
> > p4_error: latest msg from perror: Bad address
> > Killed by signal 2.
> > /opt/programs/mpich-1.2.5/bin/mpirun: line 1: 3901 Broken
> > pipe
> > /opt/programs/amber7-RH9-MPICH-FOR-LISHAN-2/exe/sander.LES "-O" "-i"
> > "md_nvt1.in" "-o" "md_nvt1.out" "-p" "ycd_1p60_les.prmtop" "-c"
> > "ycd_1p60_les.inpcrd" "-r" "md_nvt1.restrt" "-x" "md_nvt1.crd" "-e"
> > "md_nvt1.ene" -p4pg /home/yaolisha/YCD/1P60/MD_NEW/LES/PI3792 -p4wd
> > /home/yaolisha/YCD/1P60/MD_NEW/LES
> >
> >
> > Lishan
> >
> > On Wed, 2004-02-11 at 12:55, Carlos Simmerling wrote:
> > > Lishan,
> > >
> > > I used standard amber7 compiled under Linux with g77
> > > using your inputs (your crd, prmtop, etc) and it works
> > > properly. Our output files match up until I get "Single
> > > temperature bath for LES and non-LES" where you get
> > > "LES particles coupled to a separate bath". My output
> > > is the correct behavior, yours is not.
> > >
> > > I don't understand this. Did you run the sander tests after you
> > > compiled the program?
> > >
> > > Carlos
> > >
> > > ----- Original Message -----
> > > From: "Lishan Yao" <yaolisha_at_mail.msu.edu>
> > > To: <amber_at_scripps.edu>
> > > Sent: Tuesday, February 10, 2004 4:02 PM
> > > Subject: Re: AMBER: LES question
> > >
> > >
> > > > Hi:
> > > > Here are input files for two programs.
> > > >
> > > > Input file for addles.
> > > >
> > > > file rprm name=(ycd_1p60_new.prmtop) read
> > > > file rcvb name=(md_npt1.restrt) read
> > > > file wprm name=(ycd_1p60_les.prmtop) wovr
> > > > file wcrd name=(ycd_1p60_les.inpcrd) wovr
> > > > action
> > > > omas
> > > > spac numc=4 pick #mono 107 115 done
> > > > spac numc=4 pick #mono 146 156 done
> > > > spac numc=4 pick #mono 268 276 done
> > > > spac numc=4 pick #mono 307 317 done
> > > > *EOD
> > > >
> > > >
> > > > Input file for sander.LES
> > > >
> > > > molecular dynamics run
> > > > &cntrl
> > > > imin=0,irest=1,ntx=5,tempi=100.0,
> > > > ntt=1,temp0=300.0,tautp=0.5,
> > > > ntp=0,
> > > > ntb=1,ntc=2,ntf=2,
> > > > nstlim=250000,dt=0.002,
> > > > ntwe=1000,ntwx=1000,ntpr=100,
> > > > &end
> > > >
> > > >
> > > > Lishan
> > > >
> > > >
> > > >
> > > > Tue, 2004-02-10 at 16:01, Vlad Cojocaru wrote:
> > > > > Well, to me it seems that you are coupling the LES region to another
> > > > > bath. My LES protocols run properly now but I am using the same
> > > > > temperature for both LES non-LES. I guess it would be useful if you
> give
> > > > > an input file both from your addles and from your dynamics so people
> can
> > > > > judge what's up
> > > > > vlad
> > > > >
> > > > > Lishan Yao wrote:
> > > > >
> > > > > >Hi:
> > > > > > I posted this problem about two weeks ago. And I really
> appreciate
> > > > > >all the responses, which helped me solve several problems. But
> > > > > >sander.LES still can't be run correctly.
> > > > > > Here is the output I got from sander.LES. 1). The number of
> water
> > > > > >molecule is wrong. It should be about 15000. 2). The total charge
> is a
> > > > > >little bit larger than what it should be. I think something is
> wrong
> > > > > >with topology file. But I exactly follow the manual. And there is
> no
> > > > > >complaint when I run addles.What could be wrong?
> > > > > >
> > > > > >Thanks in advance.
> > > > > >
> > > > > >Best,
> > > > > >Lishan
> > > > > >
> > > > > >
> > > > > >
> > > > > > Number of triangulated 3-point waters found: 7767
> > > > > >| Atom division among processors:
> > > > > >| 0 28277 56555
> > > > > >| Running AMBER/MPI version on 2 nodes
> > > > > >
> > > > > >
> > > > > > Sum of charges from parm topology file = 0.00018743
> > > > > > Forcing neutrality...
> > > > > >
> > > > >
> > >
> >---------------------------------------------------------------------------
> > > -----
> > > > > > 4. RESULTS
> > > > >
> > >
> >---------------------------------------------------------------------------
> > > -----
> > > > > >
> > > > > ># degrees of freedom in non-LES region: 116597.
> > > > > ># degrees of freedom in LES region: 0.
> > > > > > LES particles coupled to separate bath
> > > > > > LES target temperature: 0.00
> > > > > > LES target kinetic energy: 0.00
> > > > > >non-LES target temperature: 300.00
> > > > > >non-LES target kinetic energy: 34754.19
> > > > > > ---------------------------------------------------
> > > > > > APPROXIMATING switch and d/dx switch using CUBIC SPLINE
> INTERPOLATION
> > > > > > using 5000.0 points per unit in tabled values
> > > > > > TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> > > > > >| CHECK switch(x): max rel err = 0.3242E-14 at 2.436720
> > > > > >| CHECK d/dx switch(x): max rel err = 0.8156E-11 at 2.782960
> > > > > > ---------------------------------------------------
> > > > > >
> > > > > >
> > > > > >
> > > > >
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> > > > > >
> > > >
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