[gmx-users] problem with pull code

[xy21hb]

 Dear all,
>>
>> I am pulling the saturated and unsaturated chains of a lipid bilayer to "simulate" its gel phase transition by pull code. It ends with the expected extended structure.
>>
>> But when I continue with zero pulling rate
>> to maintain the extended structure for a while, the tails go back to the original length.
>> I guess I have made some mistakes in the mdp pull code part,
>>
>> =========
>> pull                    = umbrella
>> pull-ngroups            = 6
>> pull-ncoords            = 4
>>
>> pull-group1-name        = topC2
>> pull-group2-name        = downC2
>> pull-group3-name        = topC218
>> pull-group4-name        = downC218
>> pull-group5-name        = topC316
>> pull-group6-name        = downC316
>>
>> pull-geometry    = distance      ; simple distance increase
>>
>> pull-coord1-groups      = 1 3
>> pull-coord2-groups      = 1 5
>> pull-coord3-groups      = 2 4
>> pull-coord4-groups      = 2 6
>> pull-dim         = N N Y
>>
>> pull-coord1-vec         = 0 0 1
>> pull-coord1-rate        = 0.000          ; 0.01 nm per ps = 10 nm per ns
>> pull-coord1-k           = 1000          ; kJ mol^-1 nm^-2
>> pull-coord2-vec         = 0 0 1
>> pull-coord2-rate        = 0.000          ; 0.01 nm per ps = 10 nm per ns
>> pull-coord2-k           = 1000          ; kJ mol^-1 nm^-2
>> pull-coord3-vec         = 0 0 1
>> pull-coord3-rate        = 0.000          ; 0.01 nm per ps = 10 nm per ns
>> pull-coord3-k           = 1000          ; kJ mol^-1 nm^-2
>> pull-coord4-vec         = 0 0 1
>> pull-coord4-rate        = 0.000          ; 0.01 nm per ps = 10 nm per ns
>> pull-coord4-k           = 1000          ; kJ mol^-1 nm^-2

>>
>> pull-start       = yes         ; define initial COM distance > 0
>>
>> ============
>>
>> Any guess on the reason? Many thanks.
>>
Yao







-- 
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.