[gmx-users] lipid pulling

[xy21hb]

Dear all,

 It is just I forgot to delete the pull-coord-init part.
But after I delete the followinf lines,
=======================================

>> pull-coord1-init        =  1.0
>> pull-coord2-init        =  1.0
>> pull-coord3-init        =  1.0
>> pull-coord4-init        =  1.0
>>
==============================
and keep the

" pull-start       = yes "

The problem remains. Any new idea on that?

Thanks,

Yao 










At 2016-07-07 19:43:54, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>On 7/6/16 7:24 AM, xy21hb wrote:
>> 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-coord1-init        =  1.0
>> pull-coord2-init        =  1.0
>> pull-coord3-init        =  1.0
>> pull-coord4-init        =  1.0
>>
>> pull-start       = yes         ; define initial COM distance > 0
>>
>> ============
>>
>> Any guess on the reason? Many thanks.
>>
>
>You should use pull-start = yes and not use pull-coord*-init if the lipids are 
>already in the configuration you want.  Otherwise, you're trying to set the 
>starting distance + 1.0 nm as the reference, which may not be physically 
>possible or sensible.
>
>-Justin
>
>-- 
>==================================================
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==================================================
>-- 
>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.
-- 
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.