AMBER Archive (2006)

Subject: RE: AMBER: some puzzles in equilibration MD

From: Zhihong Yu (
Date: Mon Oct 09 2006 - 10:19:15 CDT

Dear Walker
   First of all, thanks your reply!

>> gamma_ln = 5.0, (REMARKS: if I use 1.0 only, the RMS of
>> temperature is 68.96K, AVERAGE is 369.46K, the largest value
>> is 478.01K, so I use 5.0, the result got better, RMS
>> decreased to 26.16K, AVERAGE is 319.46, the largest value is
>> 396.96K. In fact, I think the temperature contorl is not very
>> satisfactory, what should I do? just keep increasing gamma_ln
>> to 10.0 or do something else?)
>This suggests that you may have a highly strained starting structure which
>is giving you problems during the trajectory. The forces are probably very
>high in one region and the thermostat can't cope with this.

>> dt = 0.001, (REMARKS: I used dt = 0.002 at the beginning,
>> but when the MD went to 398 step, error of "vlimit exceeded
>> for step 398; vmax = 128.7932, Coordinate resetting cannot be
>> accomplished, deviation is too large" took place, so I
>> decreased it to dt = 0.001, and restrained the solute only by
>> 2.0 force constant, then the MD could complete. But, when I
>> checked the md out file, I found many many "vlimit exceeded
>> for step" warnings have appeared from beginnig to ending, so
>> I wondered whether this equilibration MD is valid?
>This confirms it you have major issues with your initial structure. The fact
>that you need a 1fs time step even with shake on implies that you have some
>highly strained atoms somewhere. Try minimising the system and on step 1 see
>which atom has the highest force. Are any energy values too high? E.g. VDW,
>EEL or bond? Visualize the system and take a look at the region around atom
>reported to have the highest force. Is anything wrong here?

In fact, I've minimized the system on step1 with 500 force constant to fix the solute and relax water only, then when I went on minimizing the whole system without restraint, the procedure couldn't complete because of very very high "1-4 EEL". Therefore I checked the out file and found the strained atoms, it was a hydrogen atom of a hydroxy in a cofactor (a small organic molecule, ThDP), this cofactor has a net charge of +1, I generate its force field parameters with antechamber, gaussion 03 opt and RESP fit. Although I found this highly strained atom, what can I do then ?

>You could also try setting ntpr=1 and ntwx=1 with nstlim=200 and re-running
>your MD. This will write data to the trajectory file on every step of MD.
>You can then load this into something like VMD and visualise the movement on
>every time step. If there are structural problems it should be easy to see.

Also, most of system are stable, but a tail of the ThDP with above highly strained hydrogen atom vibrated disorderedly

>> Can I
>> perform the second NTP equilibration MD based on this MD results? )
>I wouldn't. I would fix the problems with the starting structure first.
>All the best
>|\oss Walker
>| HPC Consultant and Staff Scientist |
>| San Diego Supercomputer Center |
>| Tel: +1 858 822 0854 | EMail:- |
>| | PGP Key available on request |
>Note: Electronic Mail is not secure, has no guarantee of delivery, may not
>be read every day, and should not be used for urgent or sensitive issues.

Thanks again!

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