Hi,
I think there is a bug in some versions of VMD where reading a restart
can fail if the time is present (the second number in the second line
of the restart file). The format looks like this:
<TITLE>
<NATOM> <TIME>
<Coords> ...
Removing the TIME value should fix it. You have 2 options:
1) Remove the time value from your restart files, either with 'time
remove' before 'trajout', or by manually deleting the time value.
2) Try another format, like Netcdf restart (use the '.ncrst'
extension). This will only work if you are using VMD on linux.
-Dan
On Wed, Jan 27, 2021 at 11:00 PM 辛志宏 <xzhfood.njau.edu.cn> wrote:
>
> Dear Amber,
> I want to extract a particular snapshots (rst file) from the trajectory and then use it as a input file for umbrella sample calculation.
> I do this according to the several topic in Amber,
> http://archive.ambermd.org/201303/0382.html
> http://archive.ambermd.org/201711/0236.html
> http://archive.ambermd.org/201501/0224.html
>
>
> trajin input.nc
> trajout output.rst7 restart onlyframes 10,18,27
>
>
> The rst files were generated successfully, but it can not display in VMD, I compared the generated rst file and the rst file generated from the molecular dynamic (it can display in VMD),and find the later has some additional data at the end of section like this,
> ...........................................
> 19.1857051 -4.6555116 7.4146023 18.8220371 -5.3773736 6.9018717
> 18.4637523 -4.3729673 7.9760155 -2.4243654 -13.8058101 -21.2786187
> -1.9146608 -14.5002933 -21.6959029 -2.8608247 -13.3598833 -22.0044868
> -21.2150809 6.2174653 8.4211042 -20.7638532 6.7598422 9.0679834
> -20.6390472 6.2272326 7.6566948 24.7070281 21.5076812 1.1709882
> 25.4433883 20.9042852 1.0713951 24.3839246 21.3469960 2.0575638
> 0.2912960 0.3037410 0.0134569 -0.1705091 -0.5272947 0.0271020
> 0.4082844 0.0781819 0.5481728 0.2932252 0.3393415 -0.6883875
> -0.1237484 -0.4178922 0.9020592 1.3871243 0.2444639 -0.9532233
> 0.2631257 -0.6038555 -0.2920701 0.6753066 -0.3941904 1.2131384
> 0.2149299 0.0004143 0.4132927 0.2765796 -0.6031886 0.6400029
> 0.3344137 0.4029519 0.2140909 -0.3032180 -0.0292121 -0.0483147
> -0.2182475 0.2596782 0.4890635 0.2202241 -0.4463871 0.0644583
> 0.2769499 -0.0245921 0.0969901 -0.2766073 -0.2109181 -0.2420671
> ................................
> How can I generated the rst file correctly and display in VMD.
> I will be much appreciate if there are any sugesstion.
>
>
> Zhihong Xin
> Nanjing Agricultural University
>
>
>
>
>
>
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Received on Thu Jan 28 2021 - 07:30:04 PST
