AMBER Archive (2009)

Subject: Re: [AMBER] Strange contacts with water molecules

From: Jordan MONNET (monnet.jordan_at_free.fr)
Date: Wed Jun 17 2009 - 12:00:46 CDT

Dear all,

According to Ross's advices, I updated my protocol and I still get
some problems to look at the water...

Here is my new Production :

MD Production
  &cntrl
    igb = 0, ntb = 2, ntpr = 250, ntwx = 500,
    cut = 9.0,
    tempi = 300.0, temp0 = 300.0,
    ntt = 1, tautp = 5.0, taup = 5.0,
    ntp = 1, imin = 0,
    nstlim = 1000000, dt = 0.002,
    ntc = 2, ntf = 2, tol = 0.00000001,
    ntwr = 500, nscm = 2500,
    irest = 1, ntx = 5, iwrap = 1,
    nmropt = 1, ibelly = 0,
  &end
  &ewald
    ew_type = 0, skinnb = 1.0, nbflag = 1, use_pme = 1, vdwmeth = 1,
  &end
  &wt
    type='END',
  &end
  LISTOUT = POUT
  DISANG = R2_restraint

Here is my ptraj input :

trajin R2.mdcrd

center :1-4 mass origin
image origin center familiar

trajout all.traj trajectory

You will find as attachment a screenshot of what I see... Contacts
look now fine but as you can see, I am having some troubles with the
box. Where does it come from? Is it a visualization problem or a
simulation one?



Thank you, 

--
Jordan MONNET (3rd grade student)
Bachelor in Biology & Computer science
University of Paris Diderot (Paris VII)
Phone: +336 20 70 24 93

http://monnet.jordan.free.fr/

.·´¯`·.. ><((((º>

On Jun 9, 2009, at 10:01 AM, Jordan MONNET wrote:

> Dear Ross,
>
>> This does look pretty weird. Do you have the prmtop and original  
>> inpcrd
>> file? Plus the restart file produced by the run? This looks to me  
>> like there
>> must be some issue with the initial structure
>
> I do and it looks ok.
>
>> If you watch the trajectory file can you see where things start going
>> weird?
>
> I am not sure but it seems to become weird with the production process
>
>> ndfmin and ntcm are 'very' deprecated. I have to go back to AMBER  
>> v7.0 to
>> even find a description in the manual
>
> As you well noticed, I updated AMBER 7 to AMBER 10 but I did the
> protocol with AMBER 7 manual...
>
> Thank you so much, I will look into my input file and make it  
> better ! I guess it
> will make this strange problem disappear
> --
> Jordan MONNET (3rd grade student)
> Bachelor in Biology & Computer science
> University of Paris Diderot (Paris VII)
> Phone: +336 20 70 24 93
>
> http://monnet.jordan.free.fr/
>
> " The most exciting phrase to hear in science, the one that heralds  
> new
> discoveries, is not 'Eureka!' but 'That's funny...' "
> Isaac Asimov
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
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