[gmx-users] Non-Integral Charges

[sun]

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?
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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