[gmx-users] Non-Integral Charges

[Justin Lemkul]

On 1/13/16 7:03 AM, sun wrote:
> I am sorry i cudn't understand your question. After topology preparation and a few steps, i observe this note that system charge is non-integral. NVT and NPT run smoothly but final mdrun crashes. I have changed terminus from NH2,COOH to zwitterionic options but this reduced the charge from -5.0 to -4.9 only. I jave charged residues like Lys,Asp,Glu etc. Can you suggest something? Shall I add Na+ ions to my system? Actually i am a beginner. Would that affect my simulation?

Zwitterionic termini are for specific cases of single amino acids.  Reducing the 
charge from -5.0 to -4.9 is actually totally unphysical and even more wrong than 
what you were doing before.

Please do some simple tutorials; considerations like this are routine.

-Justin

> Regards
> Suniba
>
> Sent from my iPhone
>
>> On 13-Jan-2016, at 3:03 am, "VITALY V. CHABAN" <vvchaban at gmail.com> wrote:
>>
>> What is the charge of your infinite periodic system if your unit cell
>> charge is 5e?
>>
>>
>>
>>
>>> On Tue, Jan 12, 2016 at 11:54 AM, sun <sun.iba2 at gmail.com> wrote:
>>>
>>> Hello Everyone
>>> I want to know how to change the non-integral charges? I am simulating a
>>> pentameric model of protein in water and the net charge comes out to be
>>> -5.0. Everything goes ok till final mdrun. As soon as its started, it
>>> carshes. Is it dus to wring topology as the charges are non-integral?
>>> Please reply
>>> Suniba
>>>
>>> Sent from my iPhone
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================