[gmx-users] Re: shake vs settle for water
Rahul Godawat
godawr at rpi.edu
Wed Jun 7 22:39:57 CEST 2006
Here are the details of my .mdp file, I use PME, cutoff 1.0 nm, and time
step 2 fs...... and OS --- RedHat Enterprise Linux, I hv been using 3.2.1
for a while apart from that no specific reason for using 3.2.1
dt = 0.002 ; time step (ps)
nsteps = 100000 ; number of steps
comm_mode = Linear
comm_grps = System
energygrps = OW HW
nstcomm = 10 ; reset c.o.m. motion
nstxout = 500 ; write coords
nstvout = 500 ; write velocities
nstlog = 500 ; print to logfile
nstenergy = 500 ; print energies
nstlist = 10 ; update pairlist
ns_type = grid ; pairlist method
coulombtype = PME
rvdw = 1.0 ; cut-off for vdw
rcoulomb = 1.0 ; cut-off for coulomb
rlist = 1.0 ; cut-off for coulomb
Tcoupl = Berendsen
tc-grps = System
tau_t = 0.5
ref_t = 300
Thanks
-----Original Message-----
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Today's Topics:
1. Free volume: Pass and Gromacs (Alessandro Mattozzi)
2. Re: Free volume: Pass and Gromacs (David van der Spoel)
3. Re: Freezing part of the molecules!!! (Soren Enemark)
4. Re: Freezing part of the molecules!!! (David van der Spoel)
5. shake vs settle for water (Rahul Godawat)
6. diffusivity computations (Debashis Dutta)
7. Re: shake vs settle for water (David van der Spoel)
----------------------------------------------------------------------
Message: 1
Date: Wed, 7 Jun 2006 17:11:03 +0200
From: "Alessandro Mattozzi" <Alessandro at polymer.kth.se>
Subject: [gmx-users] Free volume: Pass and Gromacs
To: <gmx-users at gromacs.org>
Message-ID:
<B190919A5A0D684E9AC628C8574166521CFFEF at kvaser2.mimer.kth.se>
Content-Type: text/plain; charset="iso-8859-1"
Hi all
I wonder if anybody has been using Pass to measure free volume: I got these
errors:
-Error: Found an odd element (B) on atom #13454. Hydrogen radius assigned.
Suggestion: Do I have to remove all the dummies?
-Segmentation fault
Suggestion: I use trjconv to get a pdb; is it possible that I am doing some
mistake in the conversion?
Thanx
Alessandro Mattozzi
M.Phil., Ph.D. student
Dept. of Fibre and Polymer Technology
Royal Institute of Technology
Stockholm, Sweden
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Message: 2
Date: Wed, 07 Jun 2006 17:14:59 +0200
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] Free volume: Pass and Gromacs
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4486ED73.9020904 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Alessandro Mattozzi wrote:
> Hi all
> I wonder if anybody has been using Pass to measure free volume: I got
> these errors:
>
> -Error: Found an odd element (B) on atom #13454. Hydrogen radius
assigned.
> Suggestion: Do I have to remove all the dummies?
Yes.
make an index file, it will have a suitable group for it.
>
> -Segmentation fault
> Suggestion: I use trjconv to get a pdb; is it possible that I am doing
> some mistake in the conversion?
>
> Thanx
>
> Alessandro Mattozzi
> M.Phil., Ph.D. student
> Dept. of Fibre and Polymer Technology
> Royal Institute of Technology
> Stockholm, Sweden
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
------------------------------
Message: 3
Date: Wed, 7 Jun 2006 18:32:42 +0200
From: Soren Enemark <soren.enemark at polimi.it>
Subject: Re: [gmx-users] Freezing part of the molecules!!!
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <1149697962.4486ffaa9ab24 at webmail.polimi.it>
Content-Type: text/plain; charset=ISO-8859-1
Hi Marcelo,
what you need to do is:
1. create an index file (.ndx) with the groups that you want to freeze.
Such an index file should look like:
[ Group1 ]
45 46 47 48 49 ...
[ Group2 ]
106 107 ...
[ Group3 ]
....
where atoms number 45, 46, 47, 48, and 49 etc belong to your 1st group
and
so on. Remember to use the numbering as it is in the gro file.
This you can do with "make_ndx -f your_gro_file.gro"
2. Add the folling to your mdp file:
freezegrps = Group1 Group2 Group3 Group4 Group5
freezedim = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y
Note that for each group defined as freezegroup you need to specify the
dimensions that you want to freeze (x y z). This is done with either
Y or N. So if you want only to freeze Group1 in the z-direction you
write:
freezegrps = Group1
freezedim = N N Y
All the best,
Soren
Quoting Marcelo Fabricio Masman <mmasman at gmail.com>:
> Hi all!!!
>
> I am trying to run a MD simulation with part of my system frozen. I was
> looking into the manual but I couldn't find the answer since the manual
says
> the way for freezing complete groups. I would like to freeze only a part
of
> my protein and permit the completed optimization of the rest. For example,
> my protein group has 5 protein chains with 42 residues each of them. I
would
> like to freeze (in all directions) the alfa Carbon atoms for residues
18-42
> for each chain. Does somebody know if it is possible to do such thing with
> GROMACS? Can somebody help me?
>
> Thanks a lot, in advance
>
> Marcelo
>
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Message: 4
Date: Wed, 07 Jun 2006 19:27:50 +0200
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] Freezing part of the molecules!!!
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <44870C96.6010006 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Soren Enemark wrote:
> Hi Marcelo,
> what you need to do is:
>
> 1. create an index file (.ndx) with the groups that you want to freeze.
> Such an index file should look like:
> [ Group1 ]
> 45 46 47 48 49 ...
> [ Group2 ]
> 106 107 ...
> [ Group3 ]
> ....
>
> where atoms number 45, 46, 47, 48, and 49 etc belong to your 1st group
and
> so on. Remember to use the numbering as it is in the gro file.
> This you can do with "make_ndx -f your_gro_file.gro"
>
> 2. Add the folling to your mdp file:
> freezegrps = Group1 Group2 Group3 Group4 Group5
> freezedim = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y
>
> Note that for each group defined as freezegroup you need to specify
the
> dimensions that you want to freeze (x y z). This is done with either
> Y or N. So if you want only to freeze Group1 in the z-direction you
write:
> freezegrps = Group1
> freezedim = N N Y
>
> All the best,
> Soren
>
Just as a warning: please note that combining:
constraints + freeze groups + pressure coupling
will give undefined results.
> Quoting Marcelo Fabricio Masman <mmasman at gmail.com>:
>
>
>>Hi all!!!
>>
>>I am trying to run a MD simulation with part of my system frozen. I was
>>looking into the manual but I couldn't find the answer since the manual
says
>>the way for freezing complete groups. I would like to freeze only a part
of
>>my protein and permit the completed optimization of the rest. For example,
>>my protein group has 5 protein chains with 42 residues each of them. I
would
>>like to freeze (in all directions) the alfa Carbon atoms for residues
18-42
>>for each chain. Does somebody know if it is possible to do such thing with
>>GROMACS? Can somebody help me?
>>
>>Thanks a lot, in advance
>>
>>Marcelo
>>
>
>
>
>
>
> -------------------------------------------------
> This mail sent through IMP: http://horde.org/imp/
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
------------------------------
Message: 5
Date: Wed, 7 Jun 2006 13:15:24 -0400
From: "Rahul Godawat" <godawr at rpi.edu>
Subject: [gmx-users] shake vs settle for water
To: <gmx-users at gromacs.org>
Message-ID: <000701c68a55$f9f00db0$41e47180 at Rahul>
Content-Type: text/plain; charset="us-ascii"
Hi All,
I am using Groamcs 3.2.1 for my simulations, I am having some problems with
an interfacial system when I use SETTLE as opposed to SHAKE to constrain OH
bonds and HOH angle in water. As a matter of fact I did various simulations
of liquid vapor interface simulations of water, SETTLE gives me absurd
numbers while SHAKE gives consistently good results . I have looked up the
mailing list as well as manual for differences in SHAKE and SETTLE, but
apart from the statement that SETTLE Is better than SHAKE I dint find much.
Any ideas on how to resolve this.
When I look at OH bond and HOH angle distribution from SETTLE and SHAKE it's
precisely same.
Any insights would be helpful,
Thanks
Rahul
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Message: 6
Date: Wed, 07 Jun 2006 15:02:28 -0400
From: Debashis Dutta <ddutta at email.unc.edu>
Subject: [gmx-users] diffusivity computations
To: gmx-users at gromacs.org
Message-ID: <20060607150228.1ss6txv9q800wcc8 at webmail5.isis.unc.edu>
Content-Type: text/plain; charset=US-ASCII; format="flowed"
Hi,
I have trying to estimate the diffusivity of an alanine molecule
in water with the following .mdp file (for md simualtions).
; Preprocessing
title = Alanine with Water
cpp = /lib/cpp
include =
define =
; Run Control
integrator = md
tinit = 0.000
dt = 0.002
nsteps = 250000
init_step = 0
comm_mode = None
nstcomm = 1
comm_grps =
; Langevin Dynamics
; Energy Miimization
; Shell Molecular Dynamics
; Output Control
nstxout = 500
nstvout = 500
nstfout = 500
nstlog = 500
nstenergy = 500
nstxtcout = 500
xtc_precision =
energygrps = System
; Neighbor Searching
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 0.9
; Electrostatics and VdW
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 0.9
vdwtype = shift
rvdw_switch = 0
rvdw = 1.4
DispCorr = no
table-extension = 1
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
ewald_geometry = 3d
epsilon_surface = 0 optimize_fft = yes
; Temperature Coupling
tcoupl = berendsen
tc-grps = System
tau_t = 0.1
ref_t = 300
; Pressure Coupling
Pcoupl = no
pcoupltype = isotropic
tau_p = 0.5 compressibility = 4.5e-5
ref_p = 1.0
; Simulated Annealing
; Velocity Generation
gen_vel = yes
gen_temp = 300 gen_seed = 173529
; Bonds
constraints = none
constraint_algorithm = lincs
unconstrained_start = no shake_tol = 0.0001
lincs_order = 4 lincs_iter = 4
lincs_warnangle = 30
morse = no
; Energy Group Exclusions
; NMR Refinement
; Free Energy Perturbation
; Non-equilibrium MD
; Electric Fields
; User Defined Thingies
When I plot the mean square displacement, however I do not see a linear
variation with time (which is what I expected). Moreover, the estimated
diffusivity (using the g_msd command) looks reasonable (1e-5 cm^2/s)
for runs shorter than 0.1 ns. If I run it further, the diffusivity
keeps increasing to values of 1e-3 cm^2/s (for 10 ns runs). Any
comments or sugestions?
___________________________________________________________________________
------------------------------
Message: 7
Date: Wed, 07 Jun 2006 21:29:03 +0200
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] shake vs settle for water
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <448728FF.5050909 at xray.bmc.uu.se>
Content-Type: text/plain; charset=windows-1252; format=flowed
Rahul Godawat wrote:
> Hi All,
>
>
>
> I am using Groamcs 3.2.1 for my simulations, I am having some problems
> with an interfacial system when I use SETTLE as opposed to SHAKE to
> constrain OH bonds and HOH angle in water. As a matter of fact I did
> various simulations of liquid vapor interface simulations of water,
> SETTLE gives me absurd numbers while SHAKE gives consistently good
> results . I have looked up the mailing list as well as manual for
> differences in SHAKE and SETTLE, but apart from the statement that
> SETTLE Is better than SHAKE I dint find much. Any ideas on how to
> resolve this.
>
> When I look at OH bond and HOH angle distribution from SETTLE and SHAKE
> it's precisely same.
more details please.
time step, cutoffs, PME
OS
why 3.2.1?
>
> Any insights would be helpful,
>
>
>
> Thanks
>
> Rahul
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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