From: Mortaza Aghtar (m.aghtar_at_jacobs-university.de)
Date: Fri May 11 2012 - 11:29:12 CDT
Dear Ajasja,
That is true :). Reducing the time step solved the problem. Thank you.
Best,
Mortaza
On Fri, May 11, 2012 at 6:06 PM, Ajasja Ljubetič
<ajasja.ljubetic_at_gmail.com>wrote:
> Dear Mortaza,
>
> The stiffer the spring the quicker it will oscillate, so perhaps you could
> reduce your time step in order to keep the integration stable?
>
> Regards,
> Ajasja
>
>
> On 11 May 2012 17:51, Mortaza Aghtar <m.aghtar_at_jacobs-university.de>wrote:
>
>>
>> Dear all,
>> I want to run NAMD for a system with fixing length of some bonds. So I
>> did it with defining a high spring constant value for those bonds. What
>> happened was that when I define the constant values up to 15000
>> kcal/A**2/mol there is no problem for equilibrating system but bonds
>> fluctuate around 0.03 A (less than before). And when I increase the spring
>> constants there is an error about atoms moving too fast. The error is not
>> solved by either minimizing the system or setting Margin. I have two
>> questions:
>>
>> 1- Is there any other way to fix the bond lengths other than increasing
>> spring constant while it can make other problems? There might be a method
>> similar to the rigid bond option for hydrogen atoms.
>>
>> 2- If that is the only way, how can I solve the error?
>>
>> Thanks for your consideration.
>>
>> Meisam
>>
>>
>
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:58 CST