AMBER Archive (2008)

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

From: Ashish Sangwai (ashishsangwai_at_gmail.com)
Date: Fri Apr 18 2008 - 19:18:32 CDT

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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu