Just read your other responses, didnt know it would overide with vector set, but if it doesnt work try the _dim
Stephan
Gesendet: Montag, 29. Juli 2013 um 20:42 Uhr
Von: kim2811 <kmani...@iastate.edu>
An: gmx-users@gromacs.org
Betreff: [gmx-users] constant force pulling
Von: kim2811 <kmani...@iastate.edu>
An: gmx-users@gromacs.org
Betreff: [gmx-users] constant force pulling
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)
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
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.
--
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
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)
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
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.
--
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
-- 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
