Re: Re water box and system charge

From: Boyang Wang (pkuwangboyang_at_yahoo.com.cn)
Date: Fri Sep 30 2005 - 21:18:04 CDT

Why not try to neutralize by hand, not automately? Just add ions to the pdb psf files. I don't see a reason this wouldn't work. Find out the net charge of each residue, and find out what kind of ions you can add. Charged proteins should be neutralized by ions like potassium and calcium ... in the body.

snoze pa <snoze.pa_at_gmail.com> д
Well this is the problem. You can not have integer charges. check the following link

http://ftp.ks.uiuc.edu/Research/namd/mailing_list/namd-l/2488.html

I have to play with it!!!

snoze

On 9/30/05, Boyang Wang <pkuwangboyang_at_yahoo.com.cn> wrote:One solution could be adding neutralizing protons or hydroxyl anions.
I just don't understand why you would have a system charge of 4.16***, but not integer charges.

snoze pa < snoze.pa_at_gmail.com> д
thanks. So do you have any solution for this issue!!!

On 9/30/05, Boyang Wang <pkuwangboyang_at_yahoo.com.cn > wrote: I have the same question. But I guess that it is not reasonable to run the simulations for a charged system. We have to neutralize it, by acid or base, even if they don't intefere with the problem we are studying.

snoze pa <snoze.pa_at_gmail.com> д
Hi,
I fix my cluster problem and it is working now. I have another question related with water box size.
what is maximum size of water box for namd simulation..Is 10A okie for simulation?

ANother question is related with charge. My system charge before adding ions was 4.16000546655e
when I use a desired ion concentration of 0.05 mol/L then after adding 5 SOD and 9 CLA residues,
system net charge is comming 0.16e (or once can test it with 4 CL ions.. the net charge wud be .16000e)
Is it okie to run a simulation using this charge or there are other ways to fix this fractional charge(.1600054).
thanks in advance
snoze

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