From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Feb 16 2011 - 14:43:06 CST
Hi Irene, Thanks for your reply. I used different minimization step size
but the fate of the simulation was RATTLE error. So I am trying to increase
the temperature slowly in steps of 10. I will update the results if it will
On Wed, Feb 16, 2011 at 1:02 PM, wood irene <irewood_at_gmail.com> wrote:
> Sometimes, in my short experience, it happens during membranes
> May be you must to try increasing slowly the time step and temperature,
> after minimization, for 10000-20000 run steps.
> I hope to be helpful.
> 2011/2/16 snoze pa <snoze.pa_at_gmail.com>
> Dear NAMD users,
>> I am getting a constant error message in my membrane simulation. If I
>> will imersed my protein into membrane then during melting of lipids there is
>> no error message and simulation goes smoothly. However, If I will do the
>> simulation with membrane only(melting of lipids) then it crashes everytime.
>> So far I did 4 diffierent trials inculding the margin option in one of the
>> simulation but it always gives me gfollowing error message.
>> FINISHED WRITING RESTART COORDINATES
>> WRITING VELOCITIES TO RESTART FILE AT STEP 20000
>> FINISHED WRITING RESTART VELOCITIES
>> ERROR: Constraint failure in RATTLE algorithm for atom 7948!
>> ERROR: Constraint failure; simulation has become unstable.
>> ERROR: Exiting prematurely; see error messages above.
>> Even after increasing the minimization steps to 10000, it gives me the
>> similar error message for different time of the simulation.
>> After carefully checking the atoM NAME, i found the atom is C22 from the
>> lipids. So there is no error from TIP3 molecule.
>> I will highly appreciate your help to resolve this problem. I already
>> spend many cpu hours to get job done.
>> Thanks in advance.
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