[gmx-users] gas-phase protein simulation

Shi, Huilin huilshi at imail.iu.edu
Wed Nov 30 21:34:16 CET 2011


Thank you for your reply.

My concern is that if  rcoulomb and rvdw are set to be zero, does it mean that
there are no coulombic and van der waals forces involved in the simulation?

I guess there are still coulombic and van der waals forces between atoms of a single protein molecule.

Or does setting the cutoff to be zero just mean there is no forces between neighbored molecules?


From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of David van der Spoel [spoel at xray.bmc.uu.se]
Sent: Wednesday, November 30, 2011 3:00 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] gas-phase protein simulation

yes all cutoffs 0 and epsilon_rf 1 and nstlist 0 as well.

Toodle pip!

On Nov 30, 2011, at 8:39 PM, "Shi, Huilin" <huilshi at imail.iu.edu<mailto:huilshi at imail.iu.edu>> wrote:


I would like to run a gas-phase protein simulation (with charge state of  +8).
I have read this paper : Biochemistry, 2007, 47, 933-945.

In the method section of vaccum simulation, it is said
 "For the remaining parameters, the same settings were used as in the water simulations,
except that the periodic boundary conditions were turned off and no cutoffs whatsoever were used."

I am confused about "no cutoffs whatsoever were used".
Does that mean setting all the cutoffs to be zero?
In the md.mdp file, can I use the following

nstlist                  = 0
ns-type                  = simple
pbc                      = no
rlist                    = 0

coulombtype              = cut-off
rcoulomb                 = 0
epsilon_rf               = 78
epsilon_r                = 1
vdw-type                 = Cut-off
rvdw                     = 0"

Do I need to set rcoulomb/rvdw to zero or some other number?

Thank you.

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