You could use pbc get in VMD to get the cell dimensions and pbc box to see the cell covering your system. You might want to go through the following link:

http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

You can measure the cell dimension like:

set all [atomselect top all]

set mm [measure minmax $all]

set cell [vecsub [lindex $mm 1] [lindex $mm 0]]

But, actually you should already know the box size since you chose it before solvation, or? Anyway, this error is not unusual and not necessarily related to the cell size itself but more a hint to instability of the simulation.

Please let me know:

1. Is this a NPT run (do you have a barostat enabled)?

2. Which namd version are u using (is it GPU enabled)?

3. Did you minimize properly?

4. Are you using fixedatoms?

Dear Norman,

Thank you for your kind answer.

Actually, I got my cell dimensions of my system (solvated and ionized) by using similar commands using VMD:

-set all [atomselect top all]

-measure minmax $all

-measure center $all

I am afraid I did not I did not calculate correctly the CellbasisVectors in my equilibration file (attached) because I have run simulations under the same conditions but this time I got the error "Periodic cell has became too small for orginal patch grid" and this mesagge could be related to the incorrect measurement of the cell dimensions.

Regarding your questions:

1. Is this a NPT run (do you have a barostat enabled)? yes

2. Which namd version are u using (is it GPU enabled)? 2.11

3. Did you minimize properly? Yes

4. Are you using fixedatoms? YEs

Thank you for your help again,

Marlet

In the case of fixedatoms + NPT you can try to increase the barostats time constant. This is because the barostat performs box fluctuations and rescales all the atom coordinates accordingly. The fixed atoms aren't rescaled and so the other atoms are moved towards the fixed atoms which results in high repulsion potentials. If the system has more time between barostat moves, those close contacts can recover to normal and the system won't get instable. The relevant parameters are in the case of langevinpiston:

langevinpistondecay and langevinpistonperiody which have usually values of 100 and 200 fs. Increasing them by a factor of 10 should work, at least it does for me =)

All this assumes your box size is correct. Habe you checked it in VMD?

e.g.

->load PDB

pbc set {X Y Z}

pbc box -center bb

Check if the system fits into the cell actuall. Maybe make a picture too show us ;)

Dear Norman,

Yes, thank you for your sussgestions. It worked by changing those values of angevinpistondecay and langevinpistonperiod as you said.

Thank you so much for your help :)