Hi,
I don't have a periodic box. If not for the shell of water atoms, the
simulation is carried out in vacuum. Using the 100 copies I just want to
populate the tunnel. After that I am going to remove the shell of waters
and solvate the system. The minimization, equilibration etc.. were done
WITH the 100 copies. Furthermore, neutralization of the system was done
with the addition of 10 Na+ ions. Below are the input files I have used
Building the LES system
file rprm name=(center_ammonia_xd1.prmtop) read (center_ammonia_xd1.prmtop
and inpcrd are for the system with the solvation shell)
file rcrd name=(center_ammonia_xd1.inpcrd) read
file wprm name=(LES_ammonia.prmtop) wovr
file wcrd name=(LES_ammonia.inpcrd) wovr
action
omas
spac numc=100 pick #mon 996 996 done (residue 996 is the ammonia molecule)
*EOD
Minimization
LPO
&cntrl
imin = 1,ibelly=1,bellymask='1-1037', (with the bellymask I have frozen
the positions of the water molecules added by the solvateShell command)
maxcyc = 500,
ncyc = 50,
ntc = 2, ntf = 2,
igb = 0,
ntb = 0,
ntr = 1, restraint_wt = 10.0, restraintmask = '1-1037',
cut = 12,
dielc = 1,
&end
&ewald
eedmeth = 5,
&end
Heating up
LPO
&cntrl
ntx=1, irest=0,ibelly=1,bellymask='1-1037',
nsnb=1,
ntpr=100, ntwx=1000, ntwv=00,
nstlim=8000, t=0.00, dt=0.00100,
ntc = 2, ntf = 2,
ntb = 0,
ntt=1, temp0=010.0, tempi=010.0, tautp=0.0010, vlimit=20.0,
ntr = 1,
cut = 12.0,
dielc=1,
nmropt=1
/
&ewald
eedmeth = 5,
&end
&wt type='TEMP0', istep1=00000, istep2=2000, value1=000., value2=010.,
&end
&wt type='TEMP0', istep1=2001, istep2=4000, value1=010., value2=020., &end
&wt type='TEMP0', istep1=4001, istep2=6000, value1=020., value2=050., &end
&wt type='TEMP0', istep1=6001, istep2=8000, value1=050., value2=100., &end
&wt type='TEMP0', istep1=8001, istep2=10000, value1=100., value2=150.,
&end
&wt type='TEMP0', istep1=10001, istep2=12000, value1=150., value2=200.,
&end
&wt type='TEMP0', istep1=12001, istep2=14000, value1=200., value2=250.,
&end
&wt type='TEMP0', istep1=14001, istep2=16000, value1=250., value2=300.,
&end
&wt type='TEMP0', istep1=16001, istep2=18000, value1=300., value2=325.,
&end
&wt type='TEMP0', istep1=18001, istep2=20000, value1=325., value2=300.,
&end
&wt type='END' &end
HOLD PROTEIN FIXED
50.0
RES 1 1037
END
END
Equilibration
LPO
&cntrl
ntx=5, irest=1,ibelly=1,bellymask=':1-1037',
nsnb=1,
ntpr=100, ntwx=1000, ntwv=00,
nstlim=5000, t=0.00, dt=0.00100,
ntc = 2, ntf = 2,
ntb = 0,
ntt=1, temp0=300.0, tempi=300.0, tautp=1.0, vlimit=20.0,
ntr = 1,
cut = 12.0,
dielc = 1
&end
&ewald
eedmeth = 5,
&end
Hold protein fixed
40.0
RES 1 1037
END
END
In another 3 steps, the force constant was lowered successively to 30, 20
and 10kcalmol-1A-2.
Production MD (which gives problems)
LPO
&cntrl
ntx=5, irest=1,ibelly=1,bellymask=':1-1037',
nsnb=1,
ntpr=100, ntwx=1000, ntwv=00,
nstlim=170000, t=0.00, dt=0.00100,
ntc = 2, ntf = 2,
ntb = 0,
ntt=1, temp0=300.0, tempi=300.0, tautp=1.0, vlimit=20.0,
cut = 12.0,
dielc = 1,
nmropt=1
&end
&ewald
eedmeth = 5,
&end
&wt type='REST', istep1=000000,istep2=5000, &end
&wt type='END' &end /
OUTPUT
NSTEP = 100 TIME(PS) = 30.650 TEMP(K) = 315.58 PRESS =
0.0
Etot = 9561.1638 EKtot = 12382.8171 EPtot =
-2821.6533
BOND = 2878.9538 ANGLE = 7996.5073 DIHED =
10864.0766
1-4 NB = 3619.9457 1-4 EEL = 13759.1489 VDWAALS =
-6438.7749
EELEC = -35501.5108 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
==============================================================================
NSTEP = 200 TIME(PS) = 30.750 TEMP(K) = 316.59 PRESS =
0.0
Etot = 9665.6283 EKtot = 12422.2586 EPtot =
-2756.6303
BOND = 2798.4250 ANGLE = 7841.7045 DIHED =
10874.0977
1-4 NB = 3643.4607 1-4 EEL = 13858.0550 VDWAALS =
-6354.4796
EELEC = -35417.8936 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
==============================================================================
NSTEP = 300 TIME(PS) = 30.850 TEMP(K) = 316.81 PRESS =
0.0
Etot = 9645.3912 EKtot = 12430.8441 EPtot =
-2785.4528
BOND = 2799.9270 ANGLE = 7865.0760 DIHED =
10846.7443
1-4 NB = 3670.6230 1-4 EEL = 13900.2912 VDWAALS =
-6333.0907
EELEC = -35535.0236 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
==============================================================================
NSTEP = 400 TIME(PS) = 30.950 TEMP(K) = 317.15 PRESS =
0.0
Etot = 9565.3628 EKtot = 12444.5088 EPtot =
-2879.1460
BOND = 2830.6065 ANGLE = 7850.2744 DIHED =
10815.1437
1-4 NB = 3622.1353 1-4 EEL = 13862.5023 VDWAALS =
-6486.9182
EELEC = -35372.8900 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
==============================================================================
NSTEP = 500 TIME(PS) = 31.050 TEMP(K) = 311.89 PRESS =
0.0
Etot = 9638.8987 EKtot = 12237.9005 EPtot =
-2599.0018
BOND = 2881.9531 ANGLE = 7857.9620 DIHED =
10894.6733
1-4 NB = 3673.6325 1-4 EEL = 13844.7373 VDWAALS =
-6320.2943
EELEC = -35431.6657 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 600 TIME(PS) = 31.150 TEMP(K) = 312.64 PRESS =
0.0
Etot = 9401.3659 EKtot = 12267.2186 EPtot =
-2865.8527
BOND = 2794.2644 ANGLE = 7836.5540 DIHED =
10906.5111
1-4 NB = 3648.4607 1-4 EEL = 13824.1781 VDWAALS =
-6213.7574
EELEC = -35662.0637 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 700 TIME(PS) = 31.250 TEMP(K) = 312.86 PRESS =
0.0
Etot = 9444.8982 EKtot = 12275.9192 EPtot =
-2831.0210
BOND = 2802.1135 ANGLE = 7843.8829 DIHED =
10827.2407
1-4 NB = 3680.9408 1-4 EEL = 13853.7138 VDWAALS =
-6389.6106
EELEC = -35449.3021 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 800 TIME(PS) = 31.350 TEMP(K) = 313.78 PRESS =
0.0
Etot = 9322.0090 EKtot = 12312.1500 EPtot =
-2990.1410
BOND = 2810.4641 ANGLE = 7891.4186 DIHED =
10759.5069
1-4 NB = 3639.0032 1-4 EEL = 13742.0030 VDWAALS =
-6318.1405
EELEC = -35514.3963 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 900 TIME(PS) = 31.450 TEMP(K) = 311.28 PRESS =
0.0
Etot = 9444.5566 EKtot = 12213.8498 EPtot =
-2769.2932
BOND = 2796.1408 ANGLE = 7775.6385 DIHED =
10860.0099
1-4 NB = 3690.3695 1-4 EEL = 13903.7375 VDWAALS =
-6402.3100
EELEC = -35392.8794 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
MR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
=
Frac coord min, max: 0.1576021732346622 1.000169854745692
The system has extended beyond
the extent of the virtual box.
Restarting sander will recalculate
a new virtual box with 30 Angstroms
extra on each side, if there is a
restart file for this configuration.
SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
Atom out of bounds. If a restart has been written,
restarting should resolve the error
The output looks ok (If not for the error at the end, as I believe) and
when I visualize the frmaes through VMD there seems to be nothing wrong
with the structure.
Thank you
Sajeewa Dewage
On Tue, Jun 26, 2012 at 5:49 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> it's hard to help without knowing more about what you are doing. for
> example, I don't understand the solvateshell usage if you already have
> a periodic box. did you use solvent in the box?
> try to explain the steps that you took to build, equilibrate and run
> the system. was the system equilibrated and run without LES prior to
> making copies? give us the input file for the production run that has
> problems. did you carefully look at the output file to check the
> stability of the energy and temperature? make sure you do careful
> analysis- follow the tutorials if you haven't already.
>
> On Mon, Jun 25, 2012 at 12:30 PM, Sajeewa Pemasinghe
> <sajeewasp.gmail.com> wrote:
> > Hi all,
> >
>>>>>>>Message contents removed at request of author Jun-26-2012.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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Received on Tue Jun 26 2012 - 05:30:02 PDT
