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
>
>
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