From: sefer baday (SEFER.BADAY_at_unibas.ch)
Date: Mon Apr 19 2010 - 11:59:03 CDT
Thanks for the quick reply.
On 19 Apr 2010, at 18:20, Jérôme Hénin wrote:
> Hi Sefer,
> On 19 April 2010 15:49, sefer baday <SEFER.BADAY_at_unibas.ch> wrote:
>> I work on ion channel. I try to get PMF of ammonium ion moving
>> inside the
>> The reaction coordinate is the distance between ammonium ion and
>> residues in the pore, in Z-direction ( distanceZ` option ).
>> I perform the simulations on namd2.7.
>> I have few questions about my simulations.
>> 1. In my simulations, protein and lipid complex moves in z-
>> direction. Does
>> this affect the PMF calculation ?
> Not if the reaction coordinate is defined in a sensible way, i.e.
> reflects the position of the ion with respect to the pore.
>> In order to prevent this I restrained the lipid molecules by
>> applying SMD
>> constrained. I applied SMD with zero velocity hoping that
>> center of mass of lipid doesn't move.
>> SMD on
>> SMDFile abf_cons_smd.pdb
>> SMDk 10
>> SMDVel 0
>> SMDDir 1.0 1.0 1.0
>> However, for the different force constants ( for SMD ), I get
>> values of PMF.
> Do you mean you get different _converged_ values? The comparison after
> a short time might not be very informative.
Yes, I got different converged values.
I think, I shouldn't try to restrain the lipid.
>> 2. Sometimes, protein also moves in lipid. Does it also have an
>> effect on
>> ABF ?
> Hard to tell without more information... Unless the motion seems
> artefactual (e.g. far from equilibrium), it should be fine.
>> 3. In my results, the minimum value is always zero, it doesn't become
>> negative. Is this normal ?
> This is normal and purely conventional anyway. This has been discussed
> on the list recently.
>> 4. I just want to make sure that I am doing the right thing. I
>> apply ABF for
>> the both hydrogen atoms and nitrogen atom of ammonium molecule.
>> As far as I understand, if I apply only to nitrogen molecule, bond
>> nitrogen and hydrogen might affect ABF.
> This is correct.
> No problem. Please say hi to Simon for me.
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