Dear Gromacs users,
I am new to gromacs. I want to simulate a system
(protein) with a dodecahedron box in order to minimize
the time.
rlist = rcolumb = 1.2nm; (PME)
rvdw = 1.1nm; rvdw_switch = 0 (using vdwtype = switch)
so while setting the simulation box, should i give the
Thank you Tsjerk for your suggestions!
So according to this my minimal box size should be
0.6nm in order to avoid PBS effects and due to the
water effects i have to set it 1nm or higher.
So this rule is irrespective of the box type we choose
isnt it?
I got the clue for my second question.
Hi MKS,
So according to this my minimal box size should be
0.6nm in order to avoid PBS effects and due to the
water effects i have to set it 1nm or higher.
Well, not box size, but the distance from the solute to the box wall :)
So this rule is irrespective of the box type we choose
isnt
On 01/14/11, Kavyashree M hmkv...@gmail.com wrote:
Thank you Tsjerk for your suggestions!
Please leave old email context in so that people can find out what you are
talking about. Only to you is your email so important that you might remember
all the details :-)
So according to this my
Thanks Tsjerk and Mark!
After setting the box I measured the distance of the last protein
atom and the box edge it was not same all the sides. Any comments on this?
I have sent another question regarding minimization but no replys yet.
Kindly reply Sir!
Thanking you
MKS
On Fri, Jan 14, 2011
Dear Gromacs users,
I am new to gromacs. I want to simulate a system
(protein) with a dodecahedron box in order to minimize
the time.
rlist = rcolumb = 1.2nm; (PME)
rvdw = 1.1nm; rvdw_switch = 0 (using vdwtype = switch)
so when giving the simulation box, should i give the
value of
Hi MKS,
The distance between the solute and the sides of the box is separate from
the cutoffs. But, you want to have them large enough to avoid
self-interaction across the PBC. So the distance has to be set larger than
half the size of the cut-off. You probably shouldn't set it lower than 1nm
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