Re: AMBER: SHAKE in md with partial solvation

From: Ye Mei <ymei.itcc.nju.edu.cn>
Date: Sun, 5 Jun 2005 19:19:45 +0800

Ye Mei,

I also used 1fs second step in md simulation, and it stopped with the same error message but at different time.
        
Best regards,
                                 
Ye Mei
ymei.itcc.nju.edu.cn
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093
P.R.China
2005-06-05


======= 2005-06-05 15:30:00 =======

>Dear amber users
>
>I met a problem with SHAKE in md simulation of a partially solvated system. 20A TIP3P water cap is added to the peptide, around the catalytic site. All residues, including waters, that are more than 15A away from the catalytic site are not allowed to move. The system is first minimized in 2000 steps, followed by 2000 steps heat-up with step size 2fs. Then the constant temperature md simulation is performed. SHAKE is implemented in both heat-up and constant temperature md simulation. But an error message says:
>
> NSTEP = 4500 TIME(PS) = 13.000 TEMP(K) = 306.89 PRESS = 0.0
> Etot = -2812.1921 EKtot = 1628.5984 EPtot = -4440.7905
> BOND = 362.2453 ANGLE = 1021.4029 DIHED = 1348.8158
> 1-4 NB = 441.4590 1-4 EEL = 5960.7192 VDWAALS = -434.6513
> EELEC = -13140.7814 EHBOND = 0.0000 RESTRAINT = 0.0000
> ------------------------------------------------------------------------------
>
> vlimit exceeded for step 4580 ; vmax = 44.619679589066607
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 638 1406 1405
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
>Then I checked the heated structure, and found that those residues which should be kept fixed in heat-up procedure also have their coordinates changed. The constant temperature md simulation died because some hydrogens moved far away from atoms they connect to.
>Is there anything wrong with my input files in the attachment? Or how to keep those faraway residues fixed during md simulation?
>      
>
>Best regards,
>
>Ye Mei
>ymei.itcc.nju.edu.cn
>Institute of Theoretical and Computational Chemistry
>Key Laboratory of Mesoscopic Chemistry
>School of Chemistry and Chemical Engineering
>Nanjing University
>Nanjing 210093
>P.R.China
>2005-06-05
>

= = = = = = = = = = = = = = = = = = = =
                        

       
 


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jun 05 2005 - 12:53:00 PDT
Custom Search