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.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.gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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Received on Sun Apr 20 2008 - 06:07:04 PDT
