From: James Starlight (jmsstarlight_at_gmail.com)
Date: Fri Nov 08 2013 - 06:38:26 CST
Mu issue have been soled by increasing the equilibration time in the 6.6
stage up to 10ns and increasing damping coefficient from 1 ps to 2ps..
Now there are no such diffusion during production run.
James
2013/11/7 Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu>
> 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
>>>
>>>
>>>
>>
>
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:53 CST