Thanks I tried ncdump as follows:
=> ncdump -v 'cell_lengths' eq1.rst
(eq1 is heating at ntb=1, restrain =5, duration = 100ps)
output :
*cell_lengths = 85.03, 85.03, 85.03=> ncdump -v 'cell_lengths' eq2.rst *
(equilibration at ntb=2, restrain =5, duration = 40 ps)
output:
*cell_lengths = 85.0358979270415, 85.0358979270421, 85.0358979270426
=>* *ncdump
-v 'cell_lengths' eq3.rst*
(equilibration at ntb=2, restrain =2,duration = 40 ps)
*output: cell_lengths = 85.0615791538742, 85.0615791538742,
85.0615791538737*
*=> **ncdump -v 'cell_lengths' eq4.rst*
(equilibration at ntb=2, restrain =0.5, duration = 20 ps)
*Output: cell_lengths = 85.0631498869793, 85.0631498869787,
85.063149886978=> ncdump -v 'cell_lengths' prod1.rst*
(production at ntb=2, no restrain, after 31ns)
*output: cell_lengths = 85.0159297905356, 85.0159297905448,
85.0159297905427 *
*The values in rst which was generated from tleap are as:*
As a control, I checked all rst of a completely different system in which
water box was prepared in tleap (and not used from early runs)
*eq1: cell_lengths = 102.4412382, 102.4412382, 102.4412382*
*eq2: cell_lengths = 99.8934322263585, 99.8934322263601, 99.8934322263585*
*eq3: cell_lengths = 99.5095979231652, 99.5095979231659, 99.5095979231642 *
*eq4: cell_lengths = 99.2789059024954, 99.2789059024958, 99.278905902494 *
*prod1: cell_lengths = 98.9033459709183, 98.9033459709464, 98.9033459709342*
The conditions of eq1-4 were identical in both cases.
May I conclude that the system is fine because the variation which I am
seeing also exist in "standard" (see control values) run files.
Here I would like to mention that the cell_angle values were identical in
all rst files:
*cell_angles = 109.471219, 109.471219, 109.471219*
*Thanks,*
*Hirdesh*
**
On Fri, Sep 30, 2016 at 2:25 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Fri, Sep 30, 2016 at 4:53 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
> wrote:
> > .Dac: My restart file is netcdf formatted so I can not visualize it using
> > vi editor. As an alternate, I generated the inpcrd file and checked the
> > last line.
>
> FYI you could also use 'ncdump -v <variable> <file>' where <variable>
> is either 'cell_lengths' or 'cell_angles' to get the box
> lengths/angles from a NetCDF restart.
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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Received on Fri Sep 30 2016 - 06:00:04 PDT
