From: Prathit Chatterjee (
Date: Mon Nov 09 2020 - 01:14:26 CST

Thank you Prof. Freddolino for your educative comments.
Sincere Regards,

    On Monday, 9 November, 2020, 03:15:57 pm GMT+9, Peter Freddolino <> wrote:
 I think one useful step would be to actually calculate the magnitudes of the differences in coordinates between the original trajectory and the one read/written by VMD. The energy differences that you've noted here are tiny, on the order of less than one part per thousandth, and the energies are going to be very sensitive to small changes in coordinates.
I also suspect that if you actually inspect the files before/after running them through your procedure in vmd, you will find that they are in fact not the same format. Since you're using netcdf files in amber, you have a binary container format when you read them into VMD, but when you write from VMD in crdbox format, you're converting to an ascii format with different precision. Just because the file extension is .crd doesn't actually mean that the format is the same; you can see this easily enough by looking at them in any text viewer or editor. This seems likely to me to be the issue. If you want to avoid any changes you'd be best off comparing apples to apples, and having either netcdf-format or crdbox-format files both before and after vmd sees the coordinates.Best,Peter

On Sun, Nov 8, 2020 at 10:56 PM Prathit Chatterjee <> wrote:

Dear Prof. Freddolino,

Sorry for the delayed response.

The precision of selected coordinate numbers to calculate the energy is the same in both the original AMBER coordinates and protein-only generated trajectory (in VMD), and the format is .crd, calculated with cpptraj, please see below:

This is for the original amber coordinates:
trajin /homes/epsilon/users/diem/project_t-ab/traj_1/production/crd/T_310K_1_md001.crd 1 10

strip :WAT
strip :Na+
strip :Cl-

center :1-43 mass origin
image origin center familiar

pairwise IE :1-43 out pairwise_IE.out cuteelec 0.0001 cutevdw 0.0001 vmapout IE_vmap.out emapout IE_emap.out avgout IE_avg.out

This is for the protein only generated coordinates:parm
trajin /homes/epsilon/users/pchatterjee/vmd_anal_prep/diem_1/T_310K_prot_diem_1_100ns.crd 1 10

pairwise IE :1-43 out pairwise_IE.out cuteelec 0.0001 cutevdw 0.0001 vmapout IE_vmap.out emapout IE_emap.out avgout IE_avg.out

Also, I generated the protein-only amber coordinates as follows in VMD (a prototypical example provided below):
        mol new /homes/epsilon/users/diem/project_t-ab/traj_10/production/ type parm7
        mol addfile /homes/epsilon/users/diem/project_t-ab/traj_10/production/crd/T_310K_10_md$n.crd type netcdf  waitfor all

        set frames [molinfo top get numframes]
        set nf [expr {[molinfo top get numframes]-1}]

        set a [atomselect top protein]
        animate write crdbox diem_10/PHF43_310K_prot_$f.crd beg 0 end $nf waitfor all sel $a

I tried to write the protein only coordinates in several ways until reaching the above mentioned procedure, loading the original coordinates as netcdf, and writing the final protein only coordinates as crdbox.
Likewise, the coordinates of the original and protein-only coordinates could be visualized properly without noticing any apparent unnatural bonds.
Best Regards,
Prathit On Sunday, 8 November, 2020, 01:35:42 pm GMT+9, Peter Freddolino <> wrote:
 Dear Prathit,We really need more information on how you did these calculations. How were the energies calculated? And how exactly did you generate the trajectory in vmd? With such small differences it could be something as simple as a difference in the numerical precision at which coordinates were stored, depending on exactly what formats you used.Best,

On Sat, Nov 7, 2020 at 10:02 AM Prathit Chatterjee <> wrote:

 Dear VMD experts,
I had compiled a protein only amber trajectory of an explicitly solvated simulation with VMD, which I was able to visualize properly and run certain analyses with it in VMD as well.
But, for cross-checking, I tried to calculate the pairwise interaction of the original AMBER coordinates, and  the protein only generated trajectory (with VMD).
The results, although very similar, are showing certain discrepancy as follows:
[pchatterjee_at_node51 pairwise_IE]$ tail -f test*/pairwise_IE.out
==> test1/pairwise_IE.out <== [THIS IS THE ORIGINAL AMBER COORDINATE]
       1    -186.3642   -2973.0974
       2    -189.9812   -2966.1259
       3    -199.5370   -2957.7041
       4    -196.3846   -2983.7931
       5    -197.8264   -2981.1530
       6    -184.0711   -2971.6430
       7    -194.3659   -2970.1477
       8    -189.0441   -2956.9308
       9    -197.0864   -2948.2561
      10    -196.4939   -3010.1367

       1    -186.3943   -2972.9815
       2    -189.9798   -2966.1573
       3    -199.5455   -2957.6502
       4    -196.3961   -2983.7881
       5    -197.8009   -2981.1609
       6    -184.0410   -2971.7176
       7    -194.3681   -2970.0830
       8    -189.0185   -2956.9181
       9    -197.1040   -2948.2302
      10    -196.4685   -3010.0947

Although the global picture will be the same with such minor discrepancy, I just want to know for the sake of knowing what the underlying reason could be.
Any comments/suggestions will be extremely helpful.
Thank you in advance,Best Regards,Prathit