Hi Josephine,
I suggest you try lowering the force constant for your restraints.
Hope this helps
Abi Ghanem josephine wrote:
> Hi,
> I am trying to constraint angle in time-averaged protocol on a 20pb DNA.
> In the begining i did a mistake and used type='ANGAVE' for torsion angles,
> so my first question is : the value of the angles constraint i got after
> the MD, can i use them or they are wrong?
> After noticing my mistake, i used TORAVE but the problem is that my
> smulation crashed directly after less than 100 ps with the same input.
> is anybody used this kind of restraints and can give me some advice ?
> thanks for ur help,
> Josephine
>
>
> my md.in is the following:
> *************************************************************************
> ***************************** md.in *****************************
> *************************************************************************
> 200 ps MD production at constant T= 300K & P= 1Atm and coupling = 5.0
> &cntrl
> imin=0, ntx=7, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
> nscm=5000,
> ntf=2, ntc=2,
> ntb=2, ntp=1, tautp=5.0, taup=5.0,
> nstlim=100000, t=0.0, dt=0.002,
> cut=9.0,
> ntt=1,
> irest=0, nmropt=1
> &end
> # Distance restrain in time-averaged
> &wt
> type='TORAVE' , VALUE1=1.0D+5 , VALUE2=1,
> &end
> &wt
> type='TORAVI' , istep2=1,
> &end
> &wt type='END', &end
> DISANG=RMN_cont_angle
> LISTOUT=POUT
> DUMPAVE=tmp3
>
> #################################################################
> RMN_cont_angle looks like this:
> #################################################################
> # 4 THY EPSLN: (4 DT C4')-(4 DT C3')-(4 DT O3')-(5 DG P) 204 229
> &rst iat = 102, 121, 126, 127,
> r1 = 199, r2 = 204, r3 = 229, r4 = 234,
> rk2 = 10.0, rk3 = 10.0, &end
>
> # 4 THY ZETA: (4 DT C3')-(4 DT O3')-(5 DG P)-(5 DG O5') 198 234
> &rst iat = 121, 126, 127, 130,
> r1 = 193, r2 = 198, r3 = 234, r4 = 239,
> &end
>
> # 36 CYT EPSLN: (36 DC C4')-(36 DC C3')-(36 DC O3')-(37 DA P) 229 256
> &rst iat = 1117, 1134, 1139, 1140,
> r1 = 224, r2 = 229, r3 = 256, r4 = 261,
> &end
>
> # 36 CYT ZETA: (36 DC C3')-(36 DC O3')-(37 DA P)-(37 DA O5') 163 203
> &rst iat = 1134, 1139, 1140, 1143,
> r1 = 158, r2 = 163, r3 = 203, r4 = 208,
> &end
>
> ###############################################
> and the md.out of the TORAVE input gives this in the end
> ###############################################
> NSTEP = 0 TIME(PS) = 3991.000 TEMP(K) = 300.64 PRESS =
> -147.9
> Etot = -112433.9884 EKtot = 24237.2122 EPtot =
> -136671.2006
> BOND = 339.2152 ANGLE = 680.7166 DIHED =
> 775.9132
> 1-4 NB = 352.4626 1-4 EEL = -5172.6706 VDWAALS =
> 17490.2266
> EELEC = -151138.9300 EHBOND = 0.0000 RESTRAINT =
> 1.8659
> EAMBER (non-restraint) = -136673.0664
> EKCMT = 11681.3366 VIRIAL = 12970.3486 VOLUME =
> 403525.4133
> Density =
> 1.0137
> Ewald error estimate: 0.3309E-04
> ------------------------------------------------------------------------------
>
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 1.866
> ===============================================================================
>
> vlimit exceeded for step 77; vmax = 154.3507
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 37 121 122
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
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Received on Sun Oct 28 2007 - 06:07:25 PDT
