AMBER Archive (2008)

Subject: RE: AMBER: hydrogens are flying in replica exchange simulations

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Apr 19 2008 - 00:07:54 CDT

Hi Ashish,
 
Can you make sure the test cases work - both serial and parallel in
$AMBERHOME/test/
 
It sounds like there is either a bug or a compiler bug somewhere. What
hardware / OS are you running on and which compiler + version did you
compile things with?
 
All the best
Ross

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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Ashish Sangwai
Sent: Friday, April 18, 2008 17:28
To: amber_at_scripps.edu
Subject: Re: AMBER: hydrogens are flying in replica exchange simulations

Also this simulation works fine with MMTSB toolset aarexamber.pl facility.

Using inputs as

minimization

 &cntrl
   imin=1, maxcyc = 5000, ncyc = 200,
   ntx=1, irest=0, ntpr=50, ntwr=500, ntwx=0,
   ntwe=500, ntf=2, ntb=0,
   temp0 = 298.16, tempi=298.16, ntt=1,
   igb=5, tautp=1.0, ntp=0, cut=999.0,
   taup=2.0, ntc=2, saltcon = 0.0000001,
   ntrx=1, ntwprt=0, ntr=0, dt=0.002, ig=323657
 &end
END

equilibration

 &cntrl
   imin=0,
   ntx=1, irest=0, ntpr=50, ntwr=500, ntwx=0,
   ntwe=500, ntf=2, ntb=0, igb=5, nstlim=25000,
   temp0 = 298.16, tempi=298.16, ntt=1, tautp=1.0,
   ntp=0, cut=999.0, saltcon = 0.0000001,
   taup=2.0, ntc=2,
   ntrx=1,
   ntwprt=0,
   ntr=0, dt=0.002, ig=323657
 &end
END

aarexamber

sander -O -i inp0 -p 1a.prmtop -c 1a.inpcrd -o mdout0 -x mdcrd0 -r restrt0
-e mden0 -inf mdinfo0

sander -O -i inp1 -p 1a.prmtop -c restrt0 -o mdout1 -x mdcrd1 -r restrt1 -e
mden1 -inf mdinfo1

ambpdb -p 1H.prmtop < restrt1 > restrt1.pdb

set dir = output
set output = mdout.helix

aarexAmber.pl -temp 8:300:600 -par partop=1a.prmtop -mdpar
gb=obc2,nocut,dynoutfrq=50,dynseed=1071,dynsteps=500 -ensdir data
-ens lowT -n 10000 -log f00.log -amberlog $output -dir $dir restrt1.pdb &

Thanks ,

Ashish Sangwai

On Fri, Apr 18, 2008 at 7:18 PM, Ashish Sangwai <ashishsangwai_at_gmail.com>
wrote:

This does not occur for temperatures below 380K. After that for 400K, 420K
and 440K this was seem to be happening.

I tried running with rem = 0 and that run is just fine. It is happening only
when rem=1.

The averages in out files were in following way...

 NSTEP = 10000 TIME(PS) = 60.000 TEMP(K) = 495.35 PRESS =
0.0
 Etot = 56.1676 EKtot = 58.5688 EPtot =
-2.4012
 BOND = 12.3056 ANGLE = 27.2254 DIHED =
33.3567
 1-4 NB = 7.6295 1-4 EEL = 310.9982 VDWAALS =
-4.9558
 EELEC = -158.7368 EGB = -230.2240 RESTRAINT =
0.0000
 
---------------------------------------------------------------------------- 

--

Also, the simulation fails after certain point when exchange occurs with
such an unbound state with replica at 300K and AMBER stops with message 

Coordinate resetting (SHAKE) cannot be accomplished,

in between atom number 35 and 37 (alanine carbon and hydrogen) 

Also, I am doing these termini because I want to simulate a zero charge
state. And this could be a small test simulation to check how that goes. 

Thank you very much, 

Ashish Sangwai 

p.s. - nice talk at ACS New Orleans in replica exchange symposium 

On Fri, Apr 18, 2008 at 7:02 PM, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:

that is very surprising- you might want to run the same inputs but set rem=0
and remove numexchg (just normal MD) and see if you have the same
problem. I can't imagine why REMD would allow the hydrogens to move so far.
what are your energies like in the out files?

as a note, your termini are unusual... are you sure that's what you want? 

On Fri, Apr 18, 2008 at 7:43 PM, Ashish Sangwai <ashishsangwai_at_gmail.com>
wrote:

Hello, 

I am trying to carry out replica exchange simulation on polyalanine  (5 mer)
system in Generalized Born solvent. 

For replicas above 440 K, the hydrogens in the system are having unbound
co-ordinates. 

My input file looks like : 

 &cntrl
   imin=0, ntx=5, irest=1, ntxo=1, ntpr=500, ntwr=500, ntwx=200,
   ntwe=500, ntf=2, ntb=0, igb=5, nstlim=10000,
   temp0 = 300, tempi=300, ntt=2, tautp=1.0,
   ntp=0, cut=999.0, saltcon=0.001,
   taup=2.0, ntc=2, ntrx=1,
   dt=0.001, ig=323657, numexchg=500,
 &end
END

System was prepared in xleap with following commands : 

source leaprc.ff03
set default PBradii mbondi2
1a = sequence {ALA ALA ALA ALA ALA}
saveamberparm 1a 1a.prmtop 1a.inpcrd

In the most recent PDB file of REM simulation,  hydrogen co-ordinates are
unbound.....

This PDB was generated after 38 exchange attempts for a replica at 440 K.
Rest of the backbone is still  bound . 

REMARK  ALA
ATOM      1  N   ALA     1       4.380   1.257   0.972
ATOM      2  H   ALA     1     117.737 228.487 148.973
ATOM      3  CA  ALA     1       5.181   0.081   0.806
ATOM      4  HA  ALA     1      -8.373 -76.768 181.924
ATOM      5  CB  ALA     1       4.404  -0.715  -0.190
ATOM      6 1HB  ALA     1     -94.721 143.367-170.150
ATOM      7 2HB  ALA     1     258.561-362.545-208.892
ATOM      8 3HB  ALA     1    -121.572 -49.341  56.075
ATOM      9  C   ALA     1       6.711   0.289   0.471
ATOM     10  O   ALA     1       7.423  -0.676   0.212
ATOM     11  N   ALA     2       7.223   1.533   0.473
ATOM     12  H   ALA     2    -125.699 177.403  48.942
ATOM     13  CA  ALA     2       8.634   1.801   0.462
ATOM     14  HA  ALA     2     169.270-226.264-215.241
ATOM     15  CB  ALA     2       9.010   3.115  -0.180
ATOM     16 1HB  ALA     2    -311.134  87.755-407.032
ATOM     17 2HB  ALA     2     -64.133 420.606 351.098
ATOM     18 3HB  ALA     2     355.577 -48.094-155.287
ATOM     19  C   ALA     2       9.323   1.628   1.800
ATOM     20  O   ALA     2       8.714   1.354   2.846
ATOM     21  N   ALA     3      10.639   1.796   1.792
ATOM     22  H   ALA     3      55.123  15.439-100.645
ATOM     23  CA  ALA     3      11.555   2.060   2.927
ATOM     24  HA  ALA     3    -216.220 363.839 259.284
ATOM     25  CB  ALA     3      11.623   0.734   3.689
ATOM     26 1HB  ALA     3     155.952-122.441 -95.372
ATOM     27 2HB  ALA     3      79.353  44.635 188.102
ATOM     28 3HB  ALA     3    -407.256-128.682  -6.444
ATOM     29  C   ALA     3      12.963   2.618   2.563
ATOM     30  O   ALA     3      13.929   2.618   3.318
ATOM     31  N   ALA     4      13.114   3.032   1.325
ATOM     32  H   ALA     4      12.399   2.677   0.706
ATOM     33  CA  ALA     4      14.191   3.898   0.745
ATOM     34  HA  ALA     4      15.133   3.670   1.244
ATOM     35  CB  ALA     4      14.334   3.685  -0.741
ATOM     36 1HB  ALA     4      80.378-330.692 -73.240
ATOM     37 2HB  ALA     4      13.457   4.049  -1.277
ATOM     38 3HB  ALA     4      15.200   4.236  -1.108
ATOM     39  C   ALA     4      13.926   5.388   1.011
ATOM     40  O   ALA     4      14.864   6.200   1.003
ATOM     41  N   ALA     5      12.739   5.814   1.451
ATOM     42  H   ALA     5      12.045   5.089   1.560
ATOM     43  CA  ALA     5      12.360   7.109   2.018
ATOM     44  HA  ALA     5      13.242   7.714   2.229
ATOM     45  CB  ALA     5      11.627   7.902   0.925
ATOM     46 1HB  ALA     5      10.831   7.360   0.413
ATOM     47 2HB  ALA     5      11.254   8.883   1.220
ATOM     48 3HB  ALA     5      12.343   8.027   0.113
ATOM     49  C   ALA     5      11.526   6.921   3.332
ATOM     50  O   ALA     5      10.378   7.256   3.490
TER
END

Groupfile : 

-O -i inp.300 -p 1a.prmtop -c restrt.300 -r r1.300 -o out.300 -rem 1 -x
mdcrd.300
-O -i inp.320 -p 1a.prmtop -c restrt.320 -r r1.320 -o out.320 -rem 1 -x
mdcrd.320
-O -i inp.340 -p 1a.prmtop -c restrt.340 -r r1.340 -o out.340 -rem 1 -x
mdcrd.340
-O -i inp.360 -p 1a.prmtop -c restrt.360 -r r1.360 -o out.360 -rem 1 -x
mdcrd.360
-O -i inp.380 -p 1a.prmtop -c restrt.380 -r r1.380 -o out.380 -rem 1 -x
mdcrd.380
-O -i inp.400 -p 1a.prmtop -c restrt.400 -r r1.400 -o out.400 -rem 1 -x
mdcrd.400
-O -i inp.420 -p 1a.prmtop -c restrt.420 -r r1.420 -o out.420 -rem 1 -x
mdcrd.420
-O -i inp.440 -p 1a.prmtop -c restrt.440 -r r1.440 -o out.440 -rem 1 -x
mdcrd.440

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
=================================================================== 

-- 
Ashish V. Sangwai
6214 York Street
New Orleans 
LA 70125 

-- 
Ashish V. Sangwai
6214 York Street
New Orleans 
LA 70125 

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