From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Feb 22 2016 - 02:04:39 CST
The atoms can’t disappear. Maybe you just moved them out of the clipping plane. You can move the clipping plane quite easy doing the following:
1. Click into the OpenGL window.
2. Press “t” the mouse arrow should become a cross.
3. Press middle mouse button (the wheel) and move it to right and left to move the clipping plane
Another option is you used a selection by coordinates for your representation, which will of course change when moving the atoms.
Regarding “Save Coordinates” you need so select the molecule in VMD Main (just by clicking it), then “Save Coordinates” will be enabled. Another option is:
Set a [atomselect top all]
$a writepdb mynew.pdb
Von: Mihaela Drenscko [mailto:quo.physics_at_gmail.com]
Gesendet: Freitag, 19. Februar 2016 19:39
An: Norman Geist <norman.geist_at_uni-greifswald.de>
Betreff: Re: namd-l: Energy increase with fixed atoms in POPC membrane
When I use Mouse->Move->Atoms, the atoms disapear.. Does this mean they are moved? If so, I cannot "Save Coordinates". Is there any other way to to save the new coordinates, after moving these atoms?
On Thu, Feb 18, 2016 at 3:03 AM, Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> > wrote:
energies being 9999999999.9999 means they are actually infinite. This is usually caused by superimposed atoms. As you fxed some parts of your system, the superimposed atoms are probably fixed and so can’t be minimized. Try to find the atoms which are too close, maybe using the “Dynamic Bonds” representation with a small cutoff like e.g. 0.9 and unfix them or remove the clash by hand using “VMD Main->Mouse->Move->Atom” for instance.
Von: owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> [mailto:owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> ] Im Auftrag von Mihaela Drenscko
Gesendet: Mittwoch, 17. Februar 2016 23:27
An: namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
Betreff: namd-l: Energy increase with fixed atoms in POPC membrane
I was following the tutorial:
to build a POPC membrane 50x50 with PCL (instead of kcsa), using CHARMM36.
In section 3.1, page 38, it shows how fix atoms:
set fixed [atomselect top "water or name CLA POT or protein or
(chain L and name O2 P1 O3 O4 O1 C15 H52 H51 H11 C11 H12
N C14 H42 H43 H41 C12 H22 H23 H21 C13 H33 H31 H32)"]
For the membrane pdb in charmm36, there are other notaions for atoms. I made this change:
set fixed [atomselect top "water or name CLA POT or protein or \
(chain L and name O11 P O13 O14 O12 C11 H11B H11A H12A C12 H12B \
N C15 H15B H15C H15A C13 H13B H13C H13A C14 H14C H14A H14B)"]
Was this replacement wrong? When I run the jib, the energy does not minimize (I increased minimization steps to 5000, decreased timestep 1 fs, and run it for 2500 steps):
ENERGY: 7500 4446.6430 6773.7383 3764.0810 41.4892 -20222.3357 9999999999.9999 0.0000 0.0000 4719.5622 9999999999.9999 297.2827 9999999999.9999 9999999999.9999 295.0647 9999999999.9999 9999999999.9999 160380.0000 9999999999.9999 9999999999.9999
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 7500
CLOSING EXTENDED SYSTEM TRAJECTORY FILE
WRITING COORDINATES TO OUTPUT FILE AT STEP 7500
CLOSING COORDINATE DCD FILE
The last position output (seq=-2) takes 0.001 seconds, 111.801 MB of memory in use
WRITING VELOCITIES TO OUTPUT FILE AT STEP 7500
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