AMBER Archive (2008)

Subject: Re: AMBER: AMBER minimization problems

From: Lili Peng (lpeng_at_ucsd.edu)
Date: Sat Dec 20 2008 - 17:53:54 CST

Hi Ross,

Apologies for the late reply. Thanks for giving this a shot on your
machine..

I think I'll pass on the 10-year wait :). I was actually running this using
2 processors on a supercomputer cluster, rather than on a desktop, so I
don't think computer memory makes a difference(?). Your suggestions about
setting ntpr=1 to and running it using pmemd is a good idea. Can I try
using pmemd while increasing the number of processes when I run it on a
cluster?

In the meantime, I have resorted to running it in implicit solvent and the
simulations seem to be proceeding just fine. As another alternative I'm
thinking about coarse-graining the PEG polymer while retaining the explicit
solvent molecules (coarse-grained as well, of course). What do you think?

Thanks for the help,
Lili

2008/12/18 Ross Walker <ross_at_rosswalker.co.uk>

> Hi Lili,
>
>
>
> So I tried this out on my machine and have a number of comments. Firstly
> this is a HUGE system, 673,130 atoms. Running on 2 processors of my desktop
> this requires 2.6GB of memory, so unless the machine you are running this on
> has around 4GB of memory the code will be swapping like crazy which means it
> likely isn't hung it is just taking a very long time. If you wait 10 years
> or so it may actually finish. The main point is that for a simulation this
> large you will need much more than just a dual processor machine to run it.
> Firstly a advise you to use PMEMD in place of sander.MPI, this will run much
> faster and require a lot less memory (as you increase the number of
> processors).
>
>
>
> You might also want to try setting ntpr=1 - this way you will be able to
> see that the minimization hasn't stopped at 500 steps but is in fact just
> running very slowly.
>
>
>
> Also a few comments on your input file:
>
>
>
> water minimization
>
> &cntrl
>
> imin=1, ntmin=1, nmropt=0,
>
> maxcyc=2000, ncyc=500, drms=0.1
>
> ntx=1, irest=0,
>
> ntpr=500, ntwr=500, iwrap=1,
>
> ntf=1, ntb=1, cut=8.0, nsnb=10,
>
> igb=0,
>
> ibelly=0, ntr=1,
>
> restraint_wt=300.0, restraintmask=':PEG'
>
> &end
>
>
>
> nsnb=10, this has no effect on its own, sander and pmemd will build the
> list automatically as needed.
>
>
>
> restraint_wt=300.0 - this is very large. It is probably okay for the
> minimization but not for when you do MD.
>
>
>
> You will also have to use the 'old' style of specifying restraints when you
> use pmemd.
>
>
>
> Good luck,
>
> Ross
>
>
>
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Lili Peng
> *Sent:* Wednesday, December 17, 2008 8:36 AM
> *To:* amber_at_scripps.edu
> *Subject:* Re: AMBER: AMBER minimization problems
>
>
>
> Hi Ross,
>
> It just stops after the 2nd nstep and the minimization doesn't proceed any
> further. I'm attaching my minimization output for your reference.
>
> My input script was:
> /sander -O -i min_wat.in -o peg5k_wat_min_vac.out -p peg5k_wat.top -c
> peg5k_wat.crd -r peg5k_wat_min_vac.rst -ref peg5k_wat.crd
>
> My .crd and .top files are too large to attach to this email, so I've
> uploaded them to my web server here:
> http://bioengineering.ucsd.edu/~lpeng/peg/peg5k_wat.crd>
> http://bioengineering.ucsd.edu/~lpeng/peg/peg5k_wat.top>
>
> Thanks for your help,
> Lili
>
> 2008/12/17 Ross Walker <ross_at_rosswalker.co.uk>
>
> Hi Lili,
>
>
>
> What do you mean by 'ends'? Do you get any further output? Any error
> messages of any kind? It would also be helpful to see your input file.
>
>
>
> All the best
>
> Ross
>
>
>
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Lili Peng
> *Sent:* Tuesday, December 16, 2008 11:14 PM
> *To:* amber_at_scripps.edu
> *Subject:* AMBER: AMBER minimization problems
>
>
>
> Hi AMBER,
>
> I'm having trouble minimizing a 5000 Dalton polyethylene glycol molecule
> solvated in a TIP3PBOX 15 water molecules. The output file I get ends after
> the 2nd nstep of 500 (shown below). This is after I've vacuumed minimized
> my molecule (and then solvated it in water). I've attached my water
> minimization file input file. Do anyone know what the problem could be?
>
> Thanks,
> Lili
>
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> ---------------------------------------------------
> 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 = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 64267381
> | TOTAL SIZE OF NONBOND LIST = 130524253
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -2.0703E+06 1.2881E+01 4.6850E+01 O 255159
>
> BOND = 16.4676 ANGLE = 8.8005 DIHED =
> 158.2966
> VDWAALS = 255110.9185 EEL = -2325481.7410 HBOND =
> 0.0000
> 1-4 VDW = 105.8433 1-4 EEL = -249.6019 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 500 -2.6528E+06 9.0587E-01 4.5299E+00 H1 309256
>
> BOND = 182580.9181 ANGLE = 4.6033 DIHED =
> 157.3146
> VDWAALS = 382897.9872 EEL = -3218340.8995 HBOND =
> 0.0000
> 1-4 VDW = 103.2430 1-4 EEL = -249.2364 RESTRAINT =
> 3.5502
> EAMBER = -2652846.0697
>
>
>
>
>

<lilipeng_at_alum.mit.edu>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu