[gmx-users] Coordinate file for lipid bilayer
jmsstarlight at gmail.com
Thu Oct 4 15:11:08 CEST 2012
thanks for advise. Does the Packmol software suitable for generation
coordinates of the bergers ( for gromos 56 ff) lipids ? As I know
CHARMM-GUI membrane builder is suitable for only CHARMM force field
2012/10/4 Felipe Pineda, PhD <luis.pinedadecastro at lnu.se>:
> To generate starting (non-equilibrated) bilayer structures for use in MD
> simulations take a look at http://www.ime.unicamp.br/~martinez/packmol/.
> Otherwise, for conventional lipids CHARMM-GUI membrane builder
> Hope it helps!
> On 10/04/2012 07:46 AM, James Starlight wrote:
>> lastly, is there any other ways to obtain bilayers of desired
>> dimensions started from just one lipid oriented in desired way for
>> 2012/10/3, Justin Lemkul <jalemkul at vt.edu>:
>>> On 10/3/12 12:38 PM, James Starlight wrote:
>>>> thanks for advises.
>>>> Finally how I could effectively reduce size of my system (in x and y )
>>>> to the defined pbc box size ( see picture to the previous comment) ?
>>>> I've noticed that increasing of x and y to the 12 nm I obtain ideal
>>>> shape of the bilayer without miss-matches of the left and right sizes.
>>>> But when I try to decrease dimensions of that system from 12 to 8 nm
>>>> genbox -cs xz.gro -box 8.04542 8.04542 10.19156
>>>> I've obtained the system with the broadered water layers again ( as in
>>>> the picture which I've shown).
>>> My advice is still the same - you need box vectors that are compatible
>>> a sensible water layer and membrane leaflets.
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> gmx-users mailing list gmx-users at gromacs.org
>>> * 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-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> gmx-users mailing list gmx-users at gromacs.org
> * 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users