AMBER Archive (2008)

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

From: Ashish Sangwai (ashishsangwai_at_gmail.com)
Date: Sun Apr 20 2008 - 18:09:03 CDT

Hello,

I checked the $AMBERHOME/test/rem_gb_4rep/ in parallel. It works fine.

I also checked that individual MD runs (rem=0) are stable even at
temperature of 600K.

Then, I observed that 'ntf' in your test run files are 1 (total potential
calculation) even when ntc=2 (shake on).

I tried the same in my mdin files for REM and it worked. Now the hydrogens
are not dissociating.

My new mdin file looks like

&cntrl
   imin=0, ntx=5, irest=1, ntxo=1, ntpr=500, ntwr=500, ntwx=200,
   ntwe=500, ntf=1, ntb=0, igb=5, nstlim=10000,
   temp0 = 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

The problem is solved for now but I am not sure whether I should trust the
REM simulation.

Thank you very much for your help.

- Ashish Sangwai
341 Lindy Boggs Center
Chemical Engineering
Tulane University
New Orleans LA 70118

On Sat, Apr 19, 2008 at 8:49 AM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> try running a normal MD simulation at 400K or higher.
> I have never seen something like this. it also seems strange
> that your bonds are so long but the bond energy is not high-
> is that energy output you gave for one of the structures with
> dissociated hydrogen?
> also check the test cases like Ross suggested.
>
>
> On Fri, Apr 18, 2008 at 8:18 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
>
>
>
>
> --
> ===================================================================
> 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

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