*Dear users, *
*I am struggling to make a QM/MM MD start. Essentially, I minimized my
QM/MM system by using the following input :*
*Min input file:*
* 300K constant temp QMMM Min &cntrl imin=1,ntb=1, maxcyc=500,
ncyc=200, cut=8.0, ntb=1, ntc=2, ntf=2, ntpr=1,
ntwx=1,ifqnt=1 / &qmmm qmmask='.1-68', qmcharge=0, spin=1, qm_theory='EXTERN',
! Use external QM program qmshake=1, qm_ewald=0,
qm_pme=1 / &orc use_template=1 /*
*Now, I need to **extract the 220th frame and use this as restart file for
the subsequent MD. However, when outputting the trajectory into **
220th_restart.rst7
from cpptraj, I get the warning: *
Warning: Box information present in topology but not in trajectory.
*Thus, of course , when starting the dynamics, *
*the MD doesn't start because there is no box info, i.e, the error in the
output is:*
peek_ewald_inpcrd: Box info not found in inpcrd)
*This is the MD input file:*
*300K constant temp QMMMMD &cntrl imin=0, ntb=1 cut=8.0, ntc=2, ntf=2,
tempi=300.0, temp0=300.0, ntt=3, gamma_ln=1.0, nstlim=3000, dt=0.002,
ntpr=1, ntwx=1, ntwr=10,
ifqnt=1 / &qmmm qmmask='.1-68', qmcharge=0, spin=1, qm_theory='EXTERN',
! Use external QM program qmshake=1, qm_ewald=0,
qm_pme=1 / &orc use_template=1 /*
*Note that if I use the file.rst7 from the minimization, which would
correspond to the last frame, the MD goes like a charm. This makes me
thing that the box is present,*
*but there is something wrong when extracting the frame in cpptraj. In
cpptraj the way I do is:*
parm topology.prmtop
trajin trajectory.nc 200 200 1
trajout restart_200th.rst7 restart
run
Does anyone know what error could possibly be creating such issue ? Thanks
in advance.
Cheers,
Manuele
--
*Emanuele Falbo*
PhD student
Penfold group
School of Natural and Environmental Sciences
Bedson Building, Newcastle University
Newcastle upon Tyne, NE1 7RU
w: http://tompenfoldresearch.weebly.com/
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Received on Thu May 21 2020 - 08:00:01 PDT
