David,
I do notice the last line of $NAMEd.inpcrd is indeed following what I set.
The only problem is when I do a simulation. The "gap" is only present after
one step simulation. I am posting the input file here as a check:
&cntrl
imin = 0, ! no minimisation
ntx = 1, ! restart with only coordinate ( not possible in TI
setting )
irest = 0, ! no restart ( no initial velocity )
nstlim = 10,! number of steps ( 0 ns )
dt = 0.002, ! step size
ntf = 2, ! not to calculate force for SHAKE constrained bonds
ntc = 2, ! SHAKE for all hydrogen bonded
temp0 = 300.0, ! temperature
ntpr = 100, ! info frequency
ntwx = 100, ! trajectory frequency
ntwr = 100, ! restart frequency
cut = 12.0, ! cutoff
ntb = 2, ! PBC for constant pressure
ntp = 1, ! Berendsen barostat
ntt = 3, ! Langevin thermostat
gamma_ln=2.0, ! Langevin thermostta frequency
ig = -1, ! random seed
iwrap = 1, ! PBC trajectory wrapping
icfe = 1, ! Free energy calculation ( TI )
clambda = 0.0 ! lambda
klambda = 1 ! linear mixing ( required by soft-core )
ifsc = 1, ! Use soft-core potential
ntf = 1, ! complete hamiltonian ( required by soft-core )
scalpha = 0.5, ! soft-core scaling ( default )
timask1='.17,18,19,20,21,22',
timask2='.23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38',
scmask1='.17,18,19,20,21,22',
scmask2='.23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38',
/
As far as I can tell, I cannot see anything problematic here. That's why I
asked if it is a problem in tleap. The gap is very visible after
simulation, a cross with gap size ~ a few angstroms.
Simon
Simon
David A Case <david.case.rutgers.edu> 於 2018年9月4日週二 上午10:37寫道：
> On Tue, Sep 04, 2018, Simon Kit Sang Chu wrote:
>
> >
> > I just check the pdb (attached) and there was no gap.
>
> Are the coordinates different in the input pdb file and the output rst7
> or pdb file? You may need to add a "set default nocenter on" command to
> avoid a recentering of coordinates by tleap. But at most tleap would
> provide a overall translation, and would not create a "gap".
>
> >
> > The box dimension is stored in present.prmtop.
>
> The coordinates in the prmtop file are generally ignored. As I
> indicated in the previous email, you should look at the final line of
> the $NAMEd.inpcrd file you are creating. That should be the same as
> what you requested.
>
> ....dac
>
>
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Received on Tue Sep 04 2018 - 12:00:02 PDT
