VMD-L Mailing List

From: viktor drobot (linux776_at_gmail.com)
Date: Fri Sep 20 2019 - 10:51:17 CDT

No, I haven't mixed up anything (in that case VMD usually alerts me in
console).

OK, right now I'm using AmberTools19 + AMBER18 software package. You can
download my testcase from here
(https://ftp.desolve.ru/ftp/viktor/vmd_mdcrd_bug.tar.gz). A brief
explanation/details are below.

Testcase is simple alanine dipeptide system solvated with TIP3P water
(10 angstroms buffer from each side, so PBC are here). System was
prepared in tleap, here is config for leap:
source leaprc.protein.ff14SB
source leaprc.water.tip3p
peptide = sequence { ACE ALA NME }
solvatebox peptide TIP3PBOX 10.0
saveamberparm peptide system.prmtop system.inpcrd
quit

Output files are system.prmtop (according to the VMD terminology it's
"AMBER7 Parm") and system.inpcrd (I can open it in VMD if I choose
"AMBER7 Restart"; "AMBER Coordinates" or "AMBER Coordinates with
Periodic Box" doesn't work), latter is just plain text file (I can see
human-readable structure in text editor). After that I've made some
simple calculations - minimization and heating.

Step 1. Minimization

Config is:
Minimize system
  &cntrl
   imin   = 1,
   maxcyc = 10000,
   ncyc   = 5000,
   cut    = 10.0,
   ntb    = 1,
   ntc    = 1,
   ntf    = 1,
   ntpr   = 10,
   iwrap  = 1,
   ioutfm = 0
  /

Command to run (actually doesn't matter which executable is used:
sander, sander.MPI, pmemd.cuda etc):
mpirun -n 4 pmemd.MPI -O -i 01_min.in -c system.inpcrd -p system.prmtop
-o 01_min.out -r 01_min.rst

Step 2. Heating (and producing actual mdcrd)

Config is:
Heat system
  &cntrl
   imin      = 0,
   irest     = 0,
   ntx       = 1,
   nstlim    = 50000,
   dt        = 0.002,
   cut       = 10.0,
   ntb       = 1,
   ntc       = 2,
   ntf       = 2,
   ntr       = 1,
   ntt       = 3,
   ntpr      = 1000,
   ntwx      = 1000,
   ntwr      = 1000,
   nscm      = 500,
   gamma_ln  = 3.0,
   tempi     = 0.0,
   temp0     = 300.0,
   restraintmask = '!(:WAT) & !@H=',
   restraint_wt  = 10.0,
   nmropt    = 1,
   iwrap     = 1,
   ig        = -1,
   ioutfm = 0
  /

  &wt TYPE = 'TEMP0', istep1 = 0, istep2 = 50000, value1 = 0.0, value2 =
300.0 /
  &wt TYPE = 'END' /

Command to run:
mpirun -n 4 pmemd.MPI -O -i 02_heat.in -c 01_min.rst -ref 01_min.rst -p
system.prmtop -o 02_heat.out -r 02_heat.rst -x 02_heat.mdcrd

Please note that it's explicitly requested for old mdcrd format in both
config files (ioutfm = 0). After that I have 02_heat.mdcrd file - it's
just plain text file. However, I can't open it within my system.prmtop
in VMD - the problem is exactly the same as described in my first post.
You can check it by downloading my testcase archive and trying to
visualize trajectory - neither "AMBER Coordinates" nor "AMBER
Coordinates with Periodic Box" option works (in this particular case the
latter option should work because I've prepared my testcase with PBC;
however, even for simple in vacuo systems without PBCs the former
options doesn't work too).

If I convert my mdcrd to NetCDF with the help of cpptraj:
parm system.prmtop
trajin 02_heat.mdcrd
trajout 02_heat.nc
run
quit

then I'm able to open converted trajectory with my topology (converted
trajectory is in testcase archive too).

> Hi,
> Most likely you've mixed up a restart variant vs. a trajectory
> variant. We haven't made any changes to the plugins for reading
> the mdcrd files, so unless you have got the wrong file type or
> something has changed with the file structure in the particular
> version of AMBER you're using, I don't think there's actually a
> "bug" here. To determine what's going on, we would need to have a
> copy of your input files, and much more extensive details about
> how you generated them.
>
> Best regards,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Sep 20, 2019 at 05:41:40PM +0300, viktor drobot wrote:
>> Ok, where I can file a bug for this issue?