Hi,
You can not construct a WCA potential in Gromacs
by using LJ with a certain cut-off.
The cut-off with vdwtype=cut-off is the LJ neighborlist
cut-off, NOT the interaction cut-off.
To construct a WCA potential you have to use user tables.
There is one inconvience here:
if you have multiple sigm
> Date: Fri, 12 Dec 2008 17:49:29 +1100
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 56, Issue 39
>
> Manik Mayur wrote:
> > Hi Mark,
> >
> > Thanks for your reply. I used tau_t=0 for the groups to which I do not
> > wish to
00471ave/direct/01/
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Manik Mayur wrote:
Hi Mark,
Thanks for your reply. I used tau_t=0 for the groups to which I do not
wish to apply T-coupling as it was suggested in the manual. Could you
please explain what did you meant by modifying tc_grps for removal of
T-coupling for a certain group? As if I remove the spe
shahrbanoo karbalaee wrote:
Dear justin
thank you.I read pbc subject.and I know that it solve trjconv .now
if I use trjconv after premd . is it still right.?
If there is a context for this question, we don't remember it. We have
our own work and answer lots of questions. You need to make it
radhika jaswal wrote:
Hi all,
I want to calculate the energies of the protein or drug only not with
the water molecules. But edr files contain all the water md run data and
if I want to open n edit data, file doesn't gets open 'coz of the
character coding problem. If anybody has any solution
Dear justin
thank you.I read pbc subject.and I know that it solve trjconv .now
if I use trjconv after premd . is it still right.?
best
--
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Hi all,
I want to calculate the energies of the protein or drug only not with
the water molecules. But edr files contain all the water md run data
and if I want to open n edit data, file doesn't gets open 'coz of the
character coding problem. If anybody has any solution to this problem
plz sugge
Hi Mark,
Thanks for your reply. I used tau_t=0 for the groups to which I do not wish
to apply T-coupling as it was suggested in the manual. Could you please
explain what did you meant by modifying tc_grps for removal of T-coupling
for a certain group? As if I remove the specific group's name from
I did not have this issue with the cvs
> version, but once 4.0 was released I started having this trouble.
>
> Thanks in advance
>
> -Paul
>
>
>
> _
>
> -Paul
>
>
>
> _
> Express yourself instantly with MSN Messenger! Download today it's FREE!
> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
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Manik Mayur wrote:
Hi,
I am trying to remove thermostat on a certain group of atoms by taking
tau_t = 0. But upon using grompp it says:
"For proper thermostat integration tau_t (0) should be more than an
order of magnitude larger than delta_t."
And gives a warning. This was not there in v3.
I have submitted a further revision of topolbuild as file topolbuild1_2_1.tgz
This should work much better than the previous release that was rushed
on account of personal factors that threatened to preclude further work.
topolbuild 1.2.1
Reads a Tripos .mol2 file with charges to generate somethin
don't send mi a message
he
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Dear all:
Has anyone tried to run a NVE simulation for the coarse grained
dynamics using MARTINI force field? It's a little weird to me that 1fs/
step needs to be used to conserve the energy when protein is present
in the system. Does this make sense?
Thanks a lot.
Bin
--
arie wibowo wrote:
Dear all,
I want to simulate methane + water system. for methane, I just create .top file (I added #include
"methane.itp") because when I run pdb2gmx, the calculation was stop because residue
"" not found in residue topology database. but when I run grompp, the problem app
Dear all,
I want to simulate methane + water system. for methane, I just create .top file
(I added #include "methane.itp") because when I run pdb2gmx, the calculation
was stop because residue "" not found in residue topology database. but when I
run grompp, the problem appeared because library
Hi,
I was wondering if there is any way to:
1) COMM removal in a specific dimension just life freezedim. e.g. I want
COMM removal in y-direction only.
2) Get WCA potential by setting [vdw-type: Shift] and [rvdw=2^(1/6)*sigma];
As in WCA the repulsive part of LJ is retained by setting the cutoff rad
Hi,
I am trying to remove thermostat on a certain group of atoms by taking tau_t
= 0. But upon using grompp it says:
"For proper thermostat integration tau_t (0) should be more than an order of
magnitude larger than delta_t."
And gives a warning. This was not there in v3.3. Is this a bug or shoul
Hello David,
I use to follow the "rule 2" always.
However in all of these simulations, the carbon
atoms have no charge.
Well, I will do what you suggest:
Perform simulations with:
; Free energy control stuff
free_energy = yes
init_lambda = 0.00
delta_lambda =
Hi David,
I found this comment quite interesting:
"Also, if your C60 is hollow, I can imagine that it might
exclude solvent atoms from the inside, in which case you are going to
have a big convergence issue as solvent begins to interpenetrate with
the C60, which may lead to "noise" problems when
Well...
The LDFLAGS and LIBS I have set manually:
LDFLAGS = /usr/local/mopac7-1.10/src/libmopac.a
LIBS = -lxml2 -lnsl -lfftw3f -lmopac -lm -lSM -lICE -lX11
Probably, I might have confused the correct "gmxmop.f" and "dcart.f" place:
should them stay in the MOPAC folder with files and objects
It is not clear to me why you experience this problem. Perhaps post
your full .top file with .itps and your command line usage.
I did do a search for you suggesting that grompp does not like to find
ions after solvent and might produce such an error message if it does:
http://www.mail-archiv
Eudes,
On Thu, Dec 11, 2008 at 8:27 AM, Eudes Fileti <[EMAIL PROTECTED]> wrote:
> Hello David, thanks for the reply!
> I am simulating the free energy of transfer of the C60, from ethanol to
> benzene.
> The softcore parameters, I used the are the same values of Tieleman et.al.
> (nature nanotechn
Hello David, thanks for the reply!
I am simulating the free energy of transfer of the C60, from ethanol to
benzene.
The softcore parameters, I used the are the same values of Tieleman et.al.
(nature nanotechnology, 3, 363).
At figure, each curve refers to a different solvent; one of them for ethan
Hi,
Are you running in parallel with domain decomposition?
In that case it will probably not work, I forgot to add a check
for angular comm removal with domain decomposition.
It should work single cpu and with particle decomposition (mdrun -pd).
Berk
> From: [EMAIL PROTECTED]
> To: gmx-users@g
Hi again,
I am aware that it is not quite physical to do so, but in this particular
project it really helps to use such a protocol.
Indeed, it worked perfectly in 3.3, so why should that not work with 4.0? May
there be a bug in 4.0?
Regards,
Ben
>I think this question has been already address
Today's Topics:
Well, I removed that line, and "make" gone further, but I stopped in other
error:
---
make[3]: Entrando no diretório `/usr/local/gromacs-4.0.2/src/kernel'
/bin/sh ../../libtool --tag=CC  --mode=link mpicc -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused
Hi,
And if they fly away, you would probably rather have them come back on the
other side,
otherwise as your simulation length increase you slab will disappear
(unless that is the effect you are looking for, of course).
Berk
> Date: Thu, 11 Dec 2008 09:30:16 -0200
> Subject: Re: [gmx-users] PB
Dear all,
There was already a similar topic in the archive, but it didn't apply to
my case. So, could you help me with the following problem? For some
reason when I try to grompp my input, it gives the following error:
Program grompp, VERSION 3.3.2
Source code file: toppush.c, line: 835
Fatal er
Bob,
> When performing a relative binding free energy calculation, I
> understand that it is a good practice to separate the transformation
> of charges of the ligand and the transformation of vdW parameters into
> two calculations. However, is it advisable to completely discharge the
> ligand bef
Hi,
> Hi gmx-users,
> I have tried to calculate the free energy of transfer of
> a solute between two solvents by thermodynamic integration.
> However, the dgdl plot I have obtained is not smooth enough to ensure
> accuracy.
> I have used a non homogeneous spacing for lambda. The first is from 0.0
Dear Berk and Mark,
thank you for your suggestion. I will try to download that version.
regards,
Arie
--- On Wed, 12/10/08, Berk Hess <[EMAIL PROTECTED]> wrote:
> From: Berk Hess <[EMAIL PROTECTED]>
> Subject: RE: [gmx-users] fatal error during running grompp
> To: "Discussion list for GROMACS
shahrbanoo karbalaee wrote:
Dear Justin/Mark
hi
I have a system with peptide and tfe/spc .I minimized and run for
equilbrate them for 5 ns.when the pr-md was end the time.I saw the
gromac file by vmd.the peptide jump from the box .but when I saw ngmx
and choose triclinic ,the peptide was inse
as far as your forcefield and simulation parameters are consistent with
the liquid state, only a few (if any) solvent molecule should fly away
from the liquid slab.
Andre
> Hi,
>
> How is it possible a vacuum layer be maintained without solvent
> evaporation? (in absence of few solvent layers posi
Hi,
How is it possible a vacuum layer be maintained without solvent
evaporation? (in absence of few solvent layers positionally restrained
or in absence of walls which work only in pbc=xy)
Andrei
(maybe the question is trivial but I cannot figure out the answer)
On Thu, Dec 11, 2008 at 11:50 AM
Berk hess wrote:
> Your results indicate that you are running two independent mdrun processes
> simultaneously.
> Did you configure gromacs with --enable-mpi?
no ... I forgot.
thanks!
mic
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htt
Andrea Muntean wrote:
> We are using the version 3.3.3. Is there also a posibility to have pbc
> only in xy direction (as I saw it is possible in Gromacs 4.0)? The
> manual says nothing about that.
I don't think this is implemented in 3.3.3 ... but you can just
make the box length in the z-dimen
Hi Berk,
that is a good idea. Thank you for your answer.
Cheers,
Andrea
2008/12/11 Berk Hess <[EMAIL PROTECTED]>:
> Hi,
>
> This is not possible in 3.3.
>
> But in practice you almost never need this,
> since it is far more efficient to use pbc=xyz and have a slab of vacuum
> in between the peri
David van der Spoel wrote:
> If your system contains 6508 this is the whole system and that should
> not be the cause of the lincs problem.
obviously this is how far you got in reading my mail ;) ... since
a few lines further down (see below) i wrote explicitly that my
system is much larger than
Hi,
This is not possible in 3.3.
But in practice you almost never need this,
since it is far more efficient to use pbc=xyz and have a slab of vacuum
in between the periodic images in z.
Berk
> Date: Thu, 11 Dec 2008 10:30:55 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject
Hi,
Your results indicate that you are running two independent mdrun processes
simultaneously.
Did you configure gromacs with --enable-mpi?
Berk
> Date: Thu, 11 Dec 2008 01:32:14 -0800
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] with mdrun-4.0.2 and mpi output
Hi gmx-users,
We are using the version 3.3.3. Is there also a posibility to have pbc
only in xy direction (as I saw it is possible in Gromacs 4.0)? The
manual says nothing about that.
Thank you in advance.
Best regards,
Andrea
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Hi,
when i start a job with gmx version 4.0.2 as in:
mpirun -np 2 --hostfile my-hostfile mdrun_d -s topol.tpr -np 2 >& err &
then mdrun writes a traj.trr, traj.xtc and ener.edr output files, but does so
twice
so that one ends up being renamed to #ener.edr.1# etc...
it seems as if each process
Hi,
I have not heard before about such problems.
What did you do exactly?
Did you continue your simulation the old fashioned way:
tpbconv with a trajectory file?
In 4.0 there are checkpoint files which can be read by mdrun -cpi,
so you only need tpbconv to increase the number of steps in your t
Hi,
We were talking about flexible spc(e).
I would consider rigid spce the best simple water model
for biomolecular simulations.
Berk
> From: [EMAIL PROTECTED]
> Subject: Re: [gmx-users] spc_flex reference
> To: gmx-users@gromacs.org
> Date: Wed, 10 Dec 2008 22:33:37 +0100
>
> On Wed, 10 Dec
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