Pawan Kumar wrote:
Hi Xavier sir,
Thanks for your valuable reply.
How can I refine the non-bonded set-up ?
rlist, rcoulomb, rvdw as well as coulombtype. *Never* use cut-off
electrostatics for a membrane system (or really any other, for that matter).
Your results will be far less accurate than with PME (this is in the literature).
And where can I specify the time step to 0.0001 ?
dt (read the manual).
-Justin
I am new to gromacs.
Sorry to ask such questions.
Thanking you,
Pawan
On Thu, Mar 19, 2009 at 2:54 PM, <gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>> wrote:
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Today's Topics:
1. Doubt regarding membrane protein in POPC bilayer (Pawan Kumar)
2. how to get the the force plot after pulling dynamic
simulation using GMX-3.3 (huifang liu)
3. Re: Doubt regarding membrane protein in POPC bilayer
(XAvier Periole)
4. RE: compressibility tensor components, pressure coupling
anisotropic PR, triclinic systems (Berk Hess)
----------------------------------------------------------------------
Message: 1
Date: Thu, 19 Mar 2009 10:44:44 +0530
From: Pawan Kumar <pawan.chin...@gmail.com
<mailto:pawan.chin...@gmail.com>>
Subject: [gmx-users] Doubt regarding membrane protein in POPC bilayer
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Message-ID:
<143b0c640903182214n2a603f97q478bfac66f502...@mail.gmail.com
<mailto:143b0c640903182214n2a603f97q478bfac66f502...@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"
Dear gmx-users,
Greetings from Pawan.
I have modelled the structure of a protein using Modeller and then
energy
minimized using gromacs.
Then I used the popc128a bilayer from Tieleman sir's website for
inserting
the protein.
I created a bigger bilayer using the genconf command in gromacs.
I was able to minimize the bigger bilayer and then inserted my
protein in
the bilayer using the genbox command in gromacs.
I was able to minimize the system.
But when I tried to do an mdrun for few steps restraining the protein I
ended with errors like :
1) pressure scaling more than 1%
2) Warning: 1-4 interaction between 1 and 8 at distance 1.6 which is
larger
than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation.
3) too many lincs warnings.
4) Number of grid cells is zero. probably the system and the box
collapsed.
I tried to solve these errors by increasing the tau_p value for pressure
scaling error and higher table-extension value for the 1-4 interaction
warning in the mdp file but nothing is working out.
I have given the mdp files at the end for reference.
Please give me some suggestions as how to continue further.
For energy minimization:
------------------------------------
title = Protein in POPC bilayer
cpp = /usr/bin/cpp
define = -DFLEXIBLE
integrator = steep
nsteps = 50000
; Constrain control
constraints = none
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 100
nstvout = 100
nstfout = 100
; nblist update frequency
nstlist = 10
; ns algorithm
ns_type = grid
rlist = 1
; Method for doing VdW
vdw-type = Cut-off
rvdw = 1
; Method for doing electrostatics
coulombtype = Cut-off
rcoulomb = 1
; Center of mass control
nstcomm = 1
; Periodic boundary conditions
pbc = xyz
; Mode for center of mass motion removal
comm-mode = Linear
; Energy minimizing stuff
emtol = 2250
emstep = 0.001
For mdrun using position restraints:
---------------------------------------------------
title = Protein in POPC
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5000 ; total 10 ps.
nstcomm = 1
nstxout = 50
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300
; Energy monitoring
energygrps = Protein Non-Protein
; Pressure coupling is not on
Pcoupl = berendsen
tau_p = 5.0 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
Pcoupl_type = semiisotropic
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
Thanking you,
Yours sincerely,
Pawan
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Message: 2
Date: Thu, 19 Mar 2009 13:52:09 +0800
From: huifang liu <huifangliu1...@gmail.com
<mailto:huifangliu1...@gmail.com>>
Subject: [gmx-users] how to get the the force plot after pulling
dynamic simulation using GMX-3.3
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Message-ID:
<e523c6be0903182252i114666bam4bbe591a10a30...@mail.gmail.com
<mailto:e523c6be0903182252i114666bam4bbe591a10a30...@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"
I am recently doing a SMD. I think i did it very well. But i don't
know how
to get the force plot. Is there some one can give me a suggestion?
Thank you very much.
Huifang
--
Huifang Liu (Ph.D. Student)
School of Pharmacy
Fudan University
138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O)
Shanghai, China, 200032 Cell phone: +86-13764669357
E-mail: huifangliu1...@gmail.com <mailto:huifangliu1...@gmail.com>
Fax: (86-21)54237264
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Message: 3
Date: Thu, 19 Mar 2009 10:06:25 +0100
From: XAvier Periole <x.peri...@rug.nl <mailto:x.peri...@rug.nl>>
Subject: Re: [gmx-users] Doubt regarding membrane protein in POPC
bilayer
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <c85dbd34-83cd-4f4c-8a4e-5c4224cb7...@rug.nl
<mailto:c85dbd34-83cd-4f4c-8a4e-5c4224cb7...@rug.nl>>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
It is a bit difficult to guess what is exactly happening. Your
starting structure
seem to be the problem, but your topology could also be partly
responsible.
One easy thing to do is the decrease your time step to 0.0001 which
would
decrease the chances that your system explodes.
Also try to work on refining your non-bonded set-up, it looks like you
use
straight and short cut-offs.
XAvier.
On Mar 19, 2009, at 6:14 AM, Pawan Kumar wrote:
> Dear gmx-users,
>
> Greetings from Pawan.
> I have modelled the structure of a protein using Modeller and then
> energy minimized using gromacs.
> Then I used the popc128a bilayer from Tieleman sir's website for
> inserting the protein.
> I created a bigger bilayer using the genconf command in gromacs.
> I was able to minimize the bigger bilayer and then inserted my
> protein in the bilayer using the genbox command in gromacs.
> I was able to minimize the system.
> But when I tried to do an mdrun for few steps restraining the
> protein I ended with errors like :
> 1) pressure scaling more than 1%
> 2) Warning: 1-4 interaction between 1 and 8 at distance 1.6 which is
> larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation.
> 3) too many lincs warnings.
> 4) Number of grid cells is zero. probably the system and the box
> collapsed.
>
> I tried to solve these errors by increasing the tau_p value for
> pressure scaling error and higher table-extension value for the 1-4
> interaction warning in the mdp file but nothing is working out.
> I have given the mdp files at the end for reference.
> Please give me some suggestions as how to continue further.
>
> For energy minimization:
> ------------------------------------
> title = Protein in POPC bilayer
> cpp = /usr/bin/cpp
> define = -DFLEXIBLE
> integrator = steep
> nsteps = 50000
>
> ; Constrain control
> constraints = none
>
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout = 100
> nstvout = 100
> nstfout = 100
>
> ; nblist update frequency
> nstlist = 10
>
> ; ns algorithm
> ns_type = grid
> rlist = 1
>
> ; Method for doing VdW
> vdw-type = Cut-off
> rvdw = 1
>
> ; Method for doing electrostatics
> coulombtype = Cut-off
> rcoulomb = 1
>
> ; Center of mass control
> nstcomm = 1
>
> ; Periodic boundary conditions
> pbc = xyz
>
> ; Mode for center of mass motion removal
> comm-mode = Linear
>
> ; Energy minimizing stuff
> emtol = 2250
> emstep = 0.001
>
>
> For mdrun using position restraints:
> ---------------------------------------------------
> title = Protein in POPC
> cpp = /usr/bin/cpp
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 5000 ; total 10 ps.
> nstcomm = 1
> nstxout = 50
> nstvout = 1000
> nstfout = 0
> nstlog = 10
> nstenergy = 10
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> rcoulomb = 1.0
> rvdw = 1.0
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = berendsen
> tc-grps = Protein Non-Protein
> tau_t = 0.1 0.1
> ref_t = 300 300
> ; Energy monitoring
> energygrps = Protein Non-Protein
> ; Pressure coupling is not on
> Pcoupl = berendsen
> tau_p = 5.0 5.0
> compressibility = 4.5e-5 4.5e-5
> ref_p = 1.0 1.0
> Pcoupl_type = semiisotropic
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
>
> Thanking you,
>
> Yours sincerely,
> Pawan
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------
Message: 4
Date: Thu, 19 Mar 2009 10:23:27 +0100
From: Berk Hess <g...@hotmail.com <mailto:g...@hotmail.com>>
Subject: RE: [gmx-users] compressibility tensor components, pressure
coupling anisotropic PR, triclinic systems
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <col113-w6c9af5515358eb563a4798e...@phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
If you have a liquid system (no off-diagonal elasticity), you should
not use full anistropic pressure coupling.
If you have a solid system (for instance a crystal), you will have
an elastic shear stress response
and you can determine and use off-diagonal compressibility values.
You need the compressibility values to set the time scale of the
pressure coupling.
The compressibility does not affect any thermodynamic quantity, only
the dynamics.
The compressibility always occurs as a product with 1/tau_p.
If you want to determine them from a simulation, you need a
reasonable initial guess
for the compressibility and you can use a large tau_p to be on the
safe side
with the actual coupling time.
Berk
Date: Wed, 18 Mar 2009 16:02:38 -0700
From: lastexile...@yahoo.de <mailto:lastexile...@yahoo.de>
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Subject: [gmx-users] compressibility tensor components, pressure
coupling anisotropic PR, triclinic systems
Hello,
Searching first the gromacs mailing list I could not find an answer
to the problem I face.
I would like to know the vaules I have to give to the mdp file where
it asks for compressibility.
I have to conduct an NPT simulation using barostat
Parrinello-Rahman. My pressure coupling should be anisotropic. The
values I have given up to now are:
tau_p = 1.0
compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5
ref_p = 1.0 1.0 1.0 0.0 0.0 0.0
when I try to calculate the elastic constants I get reasonable
values for the diagonal elements, yet not
good for the off-diagonal. The system I have is a monoclinic one,
so giving zeros to xy,xz,yz components is not an option.
An experimental linear compressibility value I have found out is
very close to the value above, so this is why I think I get good
values in the diagonal elements.
I have found out many different questions, including one about
monoclinic systems. In one of them someone was wondering why he had
to put as input the compressibility values, while he is supposed to
calculate them from the simulation. As far as the monoclinic system
is concerned the question had to to with the components in gromacs
derived from the linear experimental values.. There was no answer to
that.
I have tried some different values myself, for the off - diagonal
components and I get either a crash of my simulation of different
results for the elastic constants. Is there an algorithm which
clearly can point me to the right direction on how to derive
the right values?
Thank you in advance,
Nikos
_________________________________________________________________
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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