On 7/29/13 2:42 PM, kim2811 wrote:
Hi,
I am trying to pull/separate a protein dimer by applying constant force in
my SMD. The dimer has dimension 9 x 8 x 5 nm^3, and I'm trying to pull in
the y-direction so I have set the box as 12 x 40 x 8 nm^3. I have also set
my simulation to run for 5 ns. However, after only 251 ps, I got this fatal
error:
Distance of pull group 1 (3.958423 nm) is larger than 0.49 times the box
size (16.314939)
This appears to be a minor output bug. The violation occurs in the z-dimension,
since 0.49 * 8 = 3.92.
Can somebody please interpret this error? When I checked the trajectory, the
protein seems to be inside the box or at least the COM of the dimer is near
the center of the box, so the protein approaching near the boundary can't be
the reason for this error. If it can help to clarify, here's my pull code:
; Pull code
pull = constant_force
pull_geometry = direction ; pull in the direction of pull code
pull_dim = Y Y Y
Note that pull_dim should be ignored here, you only need pull_vec1. The code
should interpret the .mdp contents correctly, though.
-Justin
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = chain_A ; C-terminal of Protein 1
pull_group1 = chain_B ; C-terminal of Protein 2
pull_k1 = -500 ; kJ mol^-1 nm^-1
pull_vec1 = 0 1 0
Thank you.
--
View this message in context:
http://gromacs.5086.x6.nabble.com/constant-force-pulling-tp5010180.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
