Dear all,
I have a PDB containing a protein inserted in a membrane, plus two water
layers, yielding a "cubic" unit. Here the tleap input I used to get the
parameters:
source leaprc.constphRET (<-- a customized leaprc for the cromophore)
source leaprc.lipid14
loadAmberParams frcmod.ionsjc_tip3p
monomer = loadPDB monomer.pdb
setBox monomer "vdw"
saveAmberParm monomer monomer.parm7 monomer.rst7
quit
Now..I needed to minimize, so I used this input:
&cntrl
imin = 1, ! Turn on minimization
igb = 2, ! Use the GB model CpHMD was parametrized for
saltcon = 0.1, ! Use the salt conc. CpHMD was parametrized
for
maxcyc = 5000, ! Total number of minimization cycles
icnstph = 1, ! Turn on constant pH
ntcnstph = 100000, ! Never attempt to change prot. states
cut = 1000.0, ! No cutoff
ntr = 1, ! Turn on positional restraints
restraint_wt = 10, ! 10 kcal/mol/A**2 restraint force constant
restraintmask = '!:WAT&.CA,C,O,N' ! Restraints on the backbone atoms only
ntxo = 1
/
which, obviously, didn't yield something with periodic condition (and I
need them!). I tried various combination of iwrap and other keywords, but
they didn't work/I had errors. So, first question..how do I get periodic
conditions here?
Anyway, I tried an homemade solution, coping the line containing the box
informations at the bottom of the min.rst7 and proceeded for the heating
with this input:
&cntrl
imin=0, irest=0, ntx=1,
ntpr=1000, ntwx=1000, nstlim=200000,
dt=0.002, ntt=3, gamma_ln=5.0, ig=-1,
ntc=2, ntf=2, cut=10, ntb=1,
iwrap=1, ioutfm=1, nmropt=1,
ntxo=1,
/
&wt
TYPE='TEMP0', ISTEP1=0, ISTEP2=150000,
VALUE1=10.0, VALUE2=300.0,
/
&wt TYPE='END' /
I had this error:
Error: unspecified launch failure launching kernel kClearForces
cudaFree GpuBuffer::Deallocate failed unspecified launch failure
while the mdout terminated abruptly like this:
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = 19884761.1245 EKtot = 0.0000 EPtot =
19884761.1245
BOND = 239.6294 ANGLE = 1561.7005 DIHED =
6574.9818
1-4 NB = 2276.6658 1-4 EEL = 19393.8266 VDWAALS =
20014427.1169
EELEC = -159712.7965 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
So..second question: is this happening because of my "homemade periodic
conditions solution", or the heat.mdin is simply wrong somewhere?
Here the specific of what I'm doing: I'm trying to prepare my system for
CpHMD in explicit solvent, using the CUDA code of Amber16. Can you help me?
Elisa
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 28 2016 - 14:00:03 PDT
