Re: Re:ERROR TERMINATION DUE TO SHAKE OR TORCON

From: sxzheng <sxzheng_at_mail.shcnc.ac.cn>
Date: Sat 12 Jan 2002 11:21:30 +0800

Jose Ramon Blas
It's very kindful for your response.
The problem I found can only use the electrostatic decoupling and slow growth for calculating the vdw energy method to resolve.
I have one ligand with one positive charge and a receiptor with eight negative charges to calculate the absolute free energy.
Then in water solution the system has one positive charge and zero perturbed charge and complex system has 7 negative charge and 8 negative perturbed charge.
Can you give me some advice on neutralize the system.
Should I neutralize the water solution system? If I don't neutralize the water solution system should I addions to make the complex system has zero or one positive charge?
If I use "addions unit Na+ 0" to nertralize the complex system it only adds 6 Na+ then the system has also one negative charge.Should I use "addions unit Na+ 7" to neutralize the system absolutely or "addions unit Na+ 8" to make the system has one positive charge to equil the total charge with the water solution system while not neutralize the water solution system.
Can you give me some advice ?
Best regards
zsx




02-1-7 2:33:00 д
>Hi,
>I do not know if anyone has answered your question in the AMBER list.
>I came just this morning from holidays.
>
>You may have a problem with the velocities of some atoms. Usually this
>error appears
>when two atoms are clashing. Try to find which atoms could be and reset
>their coordinates
>and/or initial velocities. The system will reach equilibrium very soon,
>less than 5 ps.
>
>Hope this helps,
>
>Blas
>
>--
>
>----------------------------------------------------------------
>----------------------------------------------------------------
>
>J.R. Blas
>
>Grup de RECONEIXEMENT MOLECULAR | e-mail:jramon_at_borzoi.bq.ub.es
>Dept.Bioquimica i Biol.Molecular | phone: + 34 93 403 58 58
>Facultat de Quimica | FAX: + 34 93 402 12 19
>Universitat de Barcelona |
>Marti i Franques,1 |
>08028 Barcelona |

                    


            sxzheng
            sxzheng_at_mail.shcnc.ac.cn
Received on Fri Jan 11 2002 - 19:21:30 PST
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