AMBER Archive (2005)

Subject: Re: RE: AMBER: SHAKE in md with partial solvation

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Tue Jun 07 2005 - 08:46:49 CDT

Dear Ross,

I tried again today. It seem that NTT=3 and GAMMA_LN=1.0 is not fit for partial solvation. NTT=1 and TAUTP = .1 sees no problem in 100ps simulation.

        
Best regards,
                                 
Ye Mei
ymei_at_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
2005-06-07

======= 2005-06-07 01:12:20 =======

>Dear Ye,
>
>> 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?
>
>Something is very wrong with your structure leading to it blowing up.
>Chances are some hydrogens are flying off too far, so far in fact that the
>SHAKE algorithm cannot correct their positions. You are going to have to
>find out what is wrong with your system. I would start by switching off
>shake and setting the time step to either 1fs or 0.5fs. Then run the
>simulation with ntwx=1 so that it records every frame to the mdcrd file. You
>can then closely watch it in something like VMD where you may be able to see
>the origin of the "blow up".
>
>You may find that belly is the cause of your problems. If you are fixing the
>residues in real high energy configurations it may be putting a huge strain
>on the rest of your system. This is especially true since you fix a lot of
>residues even during the minimisation. Try minimising without belly and then
>fix the residues, they shouldn't move far during the minimisation so it
>should cause you problems.
>
>You may need to heat your system more slowly using weight restraints.
>
>Another thing I notice is that you are using a solvent cap but you have not
>restraint energy. Have you applied all the latest bug fixes? Specifically
>bugfix.33, 40 and 43?
>
>All the best
>Ross
>
>/\
>\/
>|\oss Walker
>
>| Department of Molecular Biology TPC15 |
>| The Scripps Research Institute |
>| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
>| http://www.rosswalker.co.uk/ | 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.
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

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

　　　　　　　
 

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu