Hello,
can anybody confirm if fftw-3.1.2 is compatible with gromacs 3.3.1 and
gromacs 4.0?
A colleague has recently indicated that I must use fftw 2.1.5 for
gromacs mpi. However, I have been using fftw-3.1.2 for quite a while
now. It compiles fine and my searching today turned up some oth
I am trying to simulate slab flow 5 m/s in the x direction using the afm
pull code. I use the following parameters in the pull.ppa file with full
periodic boundary conditions.
verbose = no
runtype = afm
ngroups = 1
group_1 = water
reference_group =
weights_1 =
reference_weights =
reftype = com_t0
Hi, all,
I was wondering if there is a way to measure the shortest distance
between two groups of atoms? g_dist seems to only measure the average
distance between the two groups. Your input would be greatly
appreciated.
Sincerely,
Art Roberts
g_mindist (with or without -pi depending on what you want)
Hi, all,
I was wondering if there is a way to measure the shortest distance
between two groups of atoms? g_dist seems to only measure the
average distance between the two groups. Your input would be
greatly appreciated.
___
[EMAIL PROTECTED] a écrit :
Hello,
can anybody confirm if fftw-3.1.2 is compatible with gromacs 3.3.1 and
gromacs 4.0?
A colleague has recently indicated that I must use fftw 2.1.5 for
gromacs mpi. However, I have been using fftw-3.1.2 for quite a while
now. It compiles fine and my searchin
Hi
Could anyone please to direct me the code / the command (pdb2gmx)
, which can transfer .pdb file to .gro file?
Thank you
Lin
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[EMAIL PROTECTED] wrote:
Hello,
can anybody confirm if fftw-3.1.2 is compatible with gromacs 3.3.1 and
gromacs 4.0?
A colleague has recently indicated that I must use fftw 2.1.5 for
gromacs mpi. However, I have been using fftw-3.1.2 for quite a while
now. It compiles fine and my searching t
He, Yang wrote:
Hi Mark,
Thank you for your reply. From your point of view, I wonder whether you mean
I need to write a table based on different interaction types and then change
the source code for recognition when running my case in the gromacs.
Yes that's what I said.
I just have no
Chih-Ying Lin wrote:
Hi
Could anyone please to direct me the code / the command (pdb2gmx)
, which can transfer .pdb file to .gro file?
It's unlikely you actually need a .gro file for your purpose. pdb2gmx is
a tool for making topology files. editconf is the easiest tool for
making simple cha
Hi Mark, did you post something on this topic? There is a link
indicating that you did but it is broken for some reason. The links
above and below work fine. If you wouldn't mind, could you please
repost?
Thanks,
Chris.
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Dear Sir ,
I used your CG parameters and gromacs V3.3 to simulate protein
aggregation. And my command is :
grompp_mpi_d -np 2 -f aggre.mdp -c aggre.gro -p aggre.top -o aggre.trp
The error message is :
double-checking input for internal consistency...
Velocities were taken from a Maxwell distributio
Dear Sir ,
I used your CG parameters and gromacs V3.3 to simulate protein
aggregation. And my command is :
grompp_mpi_d -np 2 -f aggre.mdp -c aggre.gro -p aggre.top -o aggre.trp
The error message is :
double-checking input for internal consistency...
Velocities were taken from a Maxwell distributio
Dear Sir ,
I used your CG parameters and gromacs V3.3 to simulate protein
aggregation. And my command is :
grompp_mpi_d -np 2 -f aggre.mdp -c aggre.gro -p aggre.top -o aggre.trp
The error message is :
double-checking input for internal consistency...
Velocities were taken from a Maxwell distributio
Hi.
I seem having some problem in running ./pdb2gmx. Here is the output file.
Can you help me in giving me some idea to deal with this?
bcsb09s-imac52:bin bcsb09$ pdb2gmx -f 1aml.pdb -p 1aml.top -o 1aml.gro
:-) G R O M A C S (-:
Getting the Right Output Me
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: RE: [gmx-users] stochastic dynamics , langevin
> Date: Thu, 23 Oct 2008 15:32:02 -0700
>
> Along these same lines...
> (a)is there an thermostat setting in GROMACS that comes close to the DPD
> thermostat as described in (T. Sodd
Dear Users
In gromacs 4.0, in file force.c in function make_bonded_tables line
(1007)
sprintf(tabfn + strlen(basefn) - strlen(ftp2ext(efXVG)) -
1,"_%s%d.%s", tabext, i, ftp2ext(efXVG));
produces table_bonded_bonded.xvg instead of table_bonded.xvg
Greetings
Andrzej Rzepiela
Kwee Hong wrote:
Hi.
I seem having some problem in running ./pdb2gmx. Here is the output
file. Can you help me in giving me some idea to deal with this?
bcsb09s-imac52:bin bcsb09$ pdb2gmx -f 1aml.pdb -p 1aml.top -o 1aml.gro
---
Program p
Hi,
with l-bfgs minimzation, grompp always reports
WARNING 1 [file em.mdp, line unknown]:
For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
even if the mdp gives
; Method for doing electrostatics
coulombtype = PME
rcoulomb_switch = 0
rcoulomb
Jochen Hub wrote:
Hi,
with l-bfgs minimzation, grompp always reports
WARNING 1 [file em.mdp, line unknown]:
For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
even if the mdp gives
; Method for doing electrostatics
coulombtype = PME
rcoulomb_switch
Is there any eta on when the gromacs-4.0-1.src.rpm is going to show up
on:
ftp://ftp.gromacs.org/pub/gromacs/rpm
Thanks,
Mike
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Mark Abraham wrote:
> Jochen Hub wrote:
>> Hi,
>>
>> with l-bfgs minimzation, grompp always reports
>>
>> WARNING 1 [file em.mdp, line unknown]:
>> For efficient BFGS minimization, use switch/shift/pme instead of
>> cut-off.
>>
>> even if the mdp gives
>> ; Method for doing electrostatics
>> coul
Jochen Hub wrote:
Mark Abraham wrote:
Jochen Hub wrote:
Hi,
with l-bfgs minimzation, grompp always reports
WARNING 1 [file em.mdp, line unknown]:
For efficient BFGS minimization, use switch/shift/pme instead of
cut-off.
even if the mdp gives
; Method for doing electrostatics
coulombtype
Hi,
The problem is you vdwtype setting, not coulombtype.
Berk
> Date: Fri, 24 Oct 2008 16:08:14 +0200
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Warning with L-BFGS minimization
>
> Mark Abraham wrote:
> > Jochen Hub wrote:
> >> Hi,
> >>
> >> with l-bfgs m
On Fri, 2008-10-24 at 09:06 -0500, Mike Hanby wrote:
> Is there any eta on when the gromacs-4.0-1.src.rpm is going to show up
> on:
>
> ftp://ftp.gromacs.org/pub/gromacs/rpm
You may be able to use the one in Fedora, e.g.
http://download.fedora.redhat.com/pub/fedora/linux/updates/9/SRPMS.newkey/g
Thanks for the link, I'll take a look at that one. I have to build my
own RPM to compile it with Intel compilers and OpenMPI.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Jussi Lehtola
Sent: Friday, October 24, 2008 9:44 AM
To: Discussion list for GROMA
Hi Jochen,
It's probably the rvdw cutoff (from readir.c):
if (ir->eI == eiLBFGS && (ir->coulombtype==eelCUT || ir->vdwtype==evdwCUT)
&& ir->rvdw != 0) {
warning("For efficient BFGS minimization, use switch/shift/pme
instead of cut-off.");
}
Bummer!
Tsjerk
On 10/24/08, Jochen Hub <[E
Hi,
According to me it does not.
I never change the default names.
But with the default names the table file name option is "table.xvg"
and for a tabulated bond table number 0, it correctly opens "table_b0.xvg"
Berk
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Date: Fri, 24 Oct 2008
I am a novice at Gromacs (although I used Gromos 20+ years ago!)I
have a dimer with two zincs per monomer, and I get the following
complaint when running the grompp with pr.dmp, which I assume is
referring to the 4 zincs.
There are: 6789 OTHER residues
There are: 262PROT
garry wrote:
I am a novice at Gromacs (although I used Gromos 20+ years ago!)I
have a dimer with two zincs per monomer, and I get the following
complaint when running the grompp with pr.dmp, which I assume is
referring to the 4 zincs.
There are: 6789 OTHER residues
There are:
Hi
How to assign / make ionion bonds?
Thank you
Lin
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Hi, all,
Just curious. Does gromacs simulate rotation correctly? From my
observation, it would appear that every object in the simulation both
small and large has a similar rotational correlation time, which is
not reality. I would expect water for example to have an extremely
short ro
Chih-Ying Lin wrote:
Hi
How to assign / make ionion bonds?
Assign them yourself in the [ bonds ] section of the topology. As for what
parameters to assign to such a species, that's up to you; they probably don't
exist in the standard force fields within Gromacs...
-Justin
Thank you
Li
On Fri, 24 Oct 2008 10:42:26 -0700
Arthur Roberts <[EMAIL PROTECTED]> wrote:
Hi, all,
Just curious. Does gromacs simulate rotation correctly? From my
observation, it would appear that every object in the simulation both small
and large has a similar rotational correlation time, which is n
Hi
>From the following tutorial, the protein pdb file is downloaded from the
Protein Data Bank. Before running the MD simulation, we have to make sure
the structure property. I have some questions about this tutorials.
http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/
1. Make sure that there are
Hi,
I found that when the output format from editconf (gmx4) is PDB, atom
name like H5'1 will be changed to 1H5'. For other four-character atom
name like ABCD, editconf works properly.
example: editconf -f a.pdb -o b.pdb
= a.pdb ==
ATOM 1 PDT 1 -1.84
Chih-Ying Lin wrote:
Hi
From the following tutorial, the protein pdb file is downloaded from
the Protein Data Bank. Before running the MD simulation, we have to make
sure the structure property. I have some questions about this tutorials.
http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/
Garry,
I believe you are trying to not temperature couple the 4 zincs. To do this
put the 4 zincs in one group and include that group in the listing of
tc_grps and then correspondingly assign tau_t. tau_t=0 means no temperature
coupling, but I think you will also need to give a temperature for the
Wouldn't it be better to couple the Protein and Zn2+ together (i.e., index group
Protein_Zn2+)? Coupling ions separately often leads to weird
behavior/explosions when they're free in the solvent. I've never dealt with
proteins that have ions bound, so I'm curious to see what everyone else thin
Hi Lin,
Justin is right on all points. The first is indeed a check you should
always perform, but in this case (1LW9), there are no missing
residues/atoms. The point is that one should be aware that there
could. The same thing goes with the hint for the histidines. I could
have not written you sho
Hi Mark,
Thank you for your reply. From your point of view, I wonder whether you mean
I need to write a table based on different interaction types and then change
the source code for recognition when running my case in the gromacs .I just
have no idea about that .Can you give me further sugg
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