VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Sun Feb 23 2020 - 16:36:58 CST

Weird. I remember fixing some of these things when I found them impeding my
own science output, but checking the diffs with respect to the CVS, I see
that I fixed some more AMBER weirdness that never made it into the
rst7plugin. My use case always had a timestep, so even my "fixed" version
had issues with your fourth example, which I've corrected here.

See the attached version of rst7plugin.c, as well as the diff against the
current version in CVS. This will load things correctly even if a timestep
isn't present. It should just be a simple recompile once you've replaced
the file if you are in to that sort of thing, but otherwise it will depend
on how quickly John or someone with real CVS access corrects the plugin and
triggers a new alpha build to be released.

-Josh

On Sun, Feb 23, 2020 at 3:39 PM viktor drobot <linux776_at_gmail.com> wrote:

> Hi all. Recently I've been working a lot with AMBER Restart files and used
> VMD for visualizing them. I've faced one small annoying bug with VMD - it
> detects this type of input quite wrong. My AMBER version is 18 and VMD is
> 1.9.4a38.
>
> Here is <https://ftp.desolve.ru/ftp/viktor/vmd_test.tar.gz> (
> https://ftp.desolve.ru/ftp/viktor/vmd_test.tar.gz) my special test case
> which consists of 5 files: topology (*system.prmtop*), coordinates with
> timestamp (*crd.rst*), coordinates without timestamp (*crd_notime.rst*),
> coordinates and velocities with timestamp (*crdvel.rst*), coordinates and
> velocities without timestamp (*crdvel_notime.rst*). According to the specs
> <https://ambermd.org/FileFormats.php#restart> (
> https://ambermd.org/FileFormats.php#restart) timestamp field for plain
> text restarts is optional. I think restarts without timestamp are usually
> the very first input files for MD simulations right after tleap or
> something similar and restarts with timestamp are just frames grepped from
> trajectory.
>
> I load parm + crd in VMD with the following filetypes: AMBER7 Parm
> (topology) and AMBER7 Restart (coordinates). However I observe inconsistent
> behavior for some restarts. Below I'll try to illustrate it in detail.
>
>
> 1. Restart with coordinates and timestamp (*crd.rst*)
>
> When loading this combination I can see the following in console:
>
> rst7plugin) Title: Cpptraj Generated Restart
>
> rst7plugin) This file contains velocity info.
> rst7plugin) The Restartcrd has 85722 atoms.
> Info) Using plugin rst7 for coordinates from file /tmp/1/crd.rst
> rst7plugin) Importing velocities from restart file.
> Info) Finished with coordinate file /tmp/1/crd.rst.
>
> This file has no velocity info but has periodic box info. VMD tells that
> it found velocities, however periodic box isn't found. Actually it doesn't
> show anything and I see that total length of trajectory is 0. So, only
> black screen without anything useful.
>
> 2. Restart with coordinates only (*crd_notime.rst*)
>
> Console log:
>
> rst7plugin) Title: Cpptraj Generated Restart
>
> rst7plugin) This file has no velocity info.
> rst7plugin) The Restartcrd has 85722 atoms.
> rst7plugin) This restartcrd file has box info.
> rst7plugin) Box Dimensions are 84.415970 100.727646 100.317093 90.000000
> 90.000000 90.000000
> Info) Using plugin rst7 for coordinates from file /tmp/1/crd_notime.rst
> Info) Finished with coordinate file /tmp/1/crd_notime.rst.
>
> It tells that no velocities were found and reads in proper periodic box. I
> can see my molecules on the screen so that combination works fine.
>
> 3. Restart with coordinates, velocities and timestamp (*crdvel.rst*)
>
> Console output:
>
> rst7plugin) Title: Cpptraj Generated Restart
>
> rst7plugin) This file contains velocity info.
> rst7plugin) The Restartcrd has 85722 atoms.
> rst7plugin) This restartcrd file has box info.
> rst7plugin) Box Dimensions are 84.415970 100.727646 100.317093 90.000000
> 90.000000 90.000000
> Info) Using plugin rst7 for coordinates from file /tmp/1/crdvel.rst
> rst7plugin) Importing velocities from restart file.
> rst7plugin) Importing velocities from restart file.
> Info) Finished with coordinate file /tmp/1/crdvel.rst.
>
> It loads proper periodic box, detects velocities. I can see molecular
> visualization. However it tells that velocities were read two times. This
> is strange.
>
> 4. Restart with coordinates, velocities and without timestamp (
> *crdvel_notime.rst*)
>
> Info from console:
>
> rst7plugin) Title: Cpptraj Generated Restart
>
> rst7plugin) This file has no velocity info.
> rst7plugin) The Restartcrd has 85722 atoms.
> rst7plugin) This restartcrd file has box info.
> rst7plugin) Box Dimensions are -0.243004 -0.109651 0.003363 0.591160
> 0.550960 -0.262683
> Info) Using plugin rst7 for coordinates from file /tmp/1/crdvel_notime.rst
> Info) Finished with coordinate file /tmp/1/crdvel_notime.rst.
>
> It says that no velocities were found and also reads in incorrect periodic
> box. However molecular visualization is shown on the screen. Strange
> behavior too.
>
>
> Seems like VMD relies on this timestamp field during parsing. However it
> break things in some cases as shown above. I have already developed one
> tool for working with AMBER restarts and it employs another approach.
> According to the AMBER Restart specs we have the following structure of
> plain text restart (/ denotes floor integer division and % denotes modulo
> operator; so for 1 and 2 atoms in system we have only 1 line; for 3 and 4
> we have 2 lines and so on):
>
> HEADER
> NATOM TIME
> [NATOM / 2 + NATOM % 2] lines of X Y Z coordinates
> [NATOM / 2 + NATOM % 2] lines of X Y Z velocities (if any)
> PBC (if any)
>
> So we just should count total number of lines in file and then subtract 2
> (header and metadata). Let's denote (NATOM / 2 + NATOM % 2) as N and
> total number of lines in file (not counting header and metadata) as T.
> Then we have the following possibilities:
>
> 1. T = N. We have restart file with coordinates only and without
> velocities and PBC.
> 2. T = N + 1. We have restart file with coordinates and PBC, but no
> velocities are presented.
> 3. T = 2N. We have restart file with coordinates and velocities but
> without PBC.
> 4. T = 2N + 1. We have restart file with coordinates, velocities and PBC.
>
> Using this scheme VMD will open any modern AMBER Restarts correctly not
> regarding timestamp at all (which is already optional). So what do you
> think about it? Also why it reads velocities twice if they are presented?
>
> Thank you!
>