AMBER Archive (2007)

Subject: AMBER: ANGVE/TORAVE

From: Abi Ghanem josephine (josephine.abighanem_at_ibpc.fr)
Date: Thu Oct 25 2007 - 10:58:11 CDT

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. 

-- 

Josephine ABI GHANEM
IBPC, UPR 9080
13, rue P. et M. Curie,
75005 Paris, FRANCE

email: josephine.abighanem_at_ibpc.fr
tel: 01 58 41 51 67
      06 28 07 25 71

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