AMBER Archive (2008)

Subject: Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating

From: xiaonan zhang (heptoking_at_gmail.com)
Date: Tue Jun 10 2008 - 09:23:15 CDT

Thank you! Dr. Case for your suggestions

You are right, I've checked the E-bond and there are really no big rise.
And I have used desc to check the N terminal residue, they are just fine and

xleap did not report error.
As to your first suggestion, could you give me some detailed about it or
where can I find
 the relevant commands in the manual. I really have no concept on the unit
cell.

In addition, there is another question about temperature.
As the input file define the target temperature as 30K,
but mdout file showed much higher temperature,

NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 74.26 PRESS =
0.0
 Etot = -121392.2791 EKtot = 6548.3102 EPtot =
-127940.5893
 BOND = 480.4305 ANGLE = 1857.3415 DIHED =
6185.1649
 1-4 NB = 2272.4850 1-4 EEL = 27295.2989 VDWAALS =
8241.9427
 EELEC = -174273.2528 EHBOND = 0.0000 RESTRAINT =
0.0000
 Ewald error estimate: 0.4175E-05

What is the problem with it? Why the temp could not be effectively
controled?

Thank you for your help !

Best

Xiaonan

On Tue, Jun 10, 2008 at 8:50 PM, David A. Case <case_at_scripps.edu> wrote:

> On Tue, Jun 10, 2008, xiaonan zhang wrote:
>
> > Then I start minimization, everything is OK. But when I just start
> heating
> > process and visulized the trajectory with VMD. I found something very
> > strange. i.e., The two N terminal nitrogens were far away from the
> original
> > place and caused incredibly long N-H and N-C bonds.
>
> > The temperature rise to 8.87 in just 10 steps!!!
>
> This is normal: langevin thermostats reach the target temperature very
> quickly.
>
> >
> >
> > BOND = 456.6235 ANGLE = 1821.7021 DIHED =
> ^^^^^^^^^^^^
>
> You do not have a large bond energy.
>
> 1. You may have an imaging problem: that the structure is OK, the nitrogens
> involved are appearing to VMD in the wrong unit cell. This is not supposed
> to happen, but you should check anyway. Use the image command in ptraj to
> put all atoms back in the first unit cell, then visualize the molecule
> again.
>
> 2. You may be missing bonds to the N terminal nitrogens. Use the "desc"
> command in LEaP to examine the atoms in the first residue of each chain, to
> see what the nitrogens are bonded to. If some bonds are missing, then of
> course the atoms will fly away.
>
> ...good luck...dac
>
>

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