Re: Equilibration of the membrane-protein system done in CHARMM-GUI

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Wed Nov 06 2013 - 14:03:05 CST

It sounds easier and less error-prone to just let it move, then recenter
the trajectory prior to visualization/analysis.

On 11/06/2013 10:29 AM, Sunhwan Jo wrote:
> I don't think different barostat can prevent diffusion. What you need is
> cancellation of translational momentum only for your protein along XY
> dimension, but I do not know if there is any option for that in NAMD.
>
>> by the way what exactly role of the restrains in the equilibration steps
>> (some of them are defined via ColVars as I noticed)?
>
> 3 sets of restraints were used.
>
> 1. protein backbone/sidechain restraint
> 2. planar restraint that holds lipid head/tail groups in plane
> 3. dihedral restraints that retain chirality of lipid head group and
> double bonds
>
> These are used and gradually removed during STEP6. For more information,
> please read our manuscripts or tutorial.
>
> Best,
> Sunhwan
>
> On Nov 6, 2013, at 9:02 AM, James Starlight <jmsstarlight_at_gmail.com
> <mailto:jmsstarlight_at_gmail.com>> wrote:
>
>> Sunhwan.
>>
>> the RMSD have gradually increased during x-y diffusion and then
>> stabilized when protein have reached position. I suppose that Its more
>> appropriate to measure msd => Diffusion coefficent (not RMSD) from such
>> trajectory but I cant find this possibility in namd. By the way what
>> barostat options could prevent such diffusion ? ( I've tried to increase
>> constant for coupling to P_bath but there were no any changing).
>>
>> by the way what exactly role of the restrains in the equilibration steps
>> (some of them are defined via ColVars as I noticed)?
>>
>> James
>>
>>
>> 2013/11/6 Sunhwan Jo <sunhwan_at_uchicago.edu <mailto:sunhwan_at_uchicago.edu>>
>>
>> James,
>>
>> STEP7 inputs provided by CHARMM-GUI comes with no restraints. Under
>> such condition, I believe diffusion along membrane is normal. You
>> should be able to recenter the protein from the trajectory if needed.
>>
>> Your comment about increased RMSD is interesting, though. Are you
>> calculating RMSD after reorientation?
>>
>> Best,
>> Sunhwan
>>
>> On Nov 6, 2013, at 12:51 AM, James Starlight <jmsstarlight_at_gmail.com
>> <mailto:jmsstarlight_at_gmail.com>> wrote:
>>
>> > Dear all,
>> >
>> >
>> > As I've mentioned I had problems with the simulation of the
>> protein-membrane complex made in Charm-gui. Briefly I had no
>> problems during all equilibration phases but on the 7.1 ptoduction
>> run step l've observed the diffusion of the protein as the whole
>> (!!!) in the x-y plane of the membrane (analysis of the RMSD
>> provides me hight increase in RMSD (up to 10A) during first 2ns
>> when such 2D diffusion have been detected). I'm not sure if this
>> simulation was OK because I've never seen such motion in X-Y plane
>> (previously making long simulation in Gromacs with Langevins
>> dynamics and Parinello's barostat). As I've mentioned such motion
>> is observed during 7.1 step ( here any restraints are removed from
>> the conf file like
>> > # planar restraint
>> > colvars on
>> > exec sed -e "s/Constant \$fc/Constant 0/g"
>> membrane_lipid_restraint.namd.col > restraints/$outputname.col
>> > colvarsConfig restraints/$outputname.col
>> >
>> > # dihedral restraint
>> > extraBonds yes
>> > exec sed -e "s/\$FC/0/g" restraints/dihe.txt >
>> restraints/$outputname.dihe
>> > extraBondsFile restraints/$outputname.dihe
>> >
>> > Does I need more prolonged equilibration in case where I simulate
>> protein inserted in the membrane ( in comparison to the pure
>> bilayer) or may be some additional restrains should be included in
>> the 7.1 production run as well ?
>> >
>> > James
>>
>>
>

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