- "does it work? Does it give an error?"
It's not. The error is:
CMake Error at fftwBuild-stamp/extract-fftwBuild.cmake:11 (message):
error: file to extract does not exist:
- The output of cat /proc/cpuinfo:
ooker@ooker-Aspire-4741:~$ cat /proc/cpuinfo
processor : 0
vendor_id
Say you have a box with an x-side length of 3 nm and two atoms with x-dimension
position restraints to: (a) x=1 nm, and (b) x=2 nm
Then let the box shrink to 99% of its previous size due to pressure coupling.
The following is my understanding of the locations to which the atoms will be
restrai
That surprises me. Arnau Cordomí was very responsive when I requested the files
a year ago (he sent them within 24 hours). Did you email Arnau ? I didn't ask
for permission to redistribute the files, so I can't post them to you, but I
suspect that you can get them if you ask Arnau. It's probably
Thanks, Justin. I am trying to understand what is meant by 'com' option.
Following two sentences in manual seem conflicting with each other:
"*Scale* the center of mass of the reference coordinates with the scaling
matrix of the pressure coupling. The *vectors of each reference
coordinate*to the c
Dear Chris
Sorry, That didn't solve my problem. I tried that option ,before posting
here, with different authors from two publications, but seems no reply from
anybody. I wish, I could find somebody in this mailing list who is willing
to put forward his/her advice or share their experience with me
The structure was equilibrated by an 30 ns NPT, and the structure is well
equilibrated,
in the .log file appear this
Step Time Lambda
8000 16.00.0
Energies (kJ/mol)
AngleProper Dih. Ryckaert-Bell. Improper Dih.
On 3/24/14, 9:05 PM, Chetan Mahajan wrote:
Hi Justin,
My system is TiO2 crystal (2160 atoms position restrained) solvated by 3656
water molecules, 1 formate anion and 1 sodium ion. Is it true that when
'all' option is used, positions of the atoms (meant to be restrained)
always change?
Con
On 3/24/14, 8:56 PM, Andres Ortega wrote:
Dear gromacs users, i ´ve beem trying to get the geometries of a drug
molecule permeating an ion channel,
the drug molecule is in a greater Z position than the Protein, but i always
get the error :"Segmentation fault (core dumped)"
Does the simulation
Hi Justin,
My system is TiO2 crystal (2160 atoms position restrained) solvated by 3656
water molecules, 1 formate anion and 1 sodium ion. Is it true that when
'all' option is used, positions of the atoms (meant to be restrained)
always change?
Thanks
Chetan
On Mon, Mar 24, 2014 at 7:37 PM, Jus
Dear gromacs users, i ´ve beem trying to get the geometries of a drug
molecule permeating an ion channel,
the drug molecule is in a greater Z position than the Protein, but i always
get the error :"Segmentation fault (core dumped)"
this is my .mdp
title = Umbrella pulling simulation DOX
; Ru
On 3/24/14, 8:29 PM, Chetan Mahajan wrote:
Thanks, Mark. So is 'all' option okay when positions of each of the atoms
of TiO2 crystal (2160 atoms total) are restrained in space? Apparently, it
does not seem correct, since positions of the atoms of TiO2 crystal change
when 'all' option is applied
Thanks, Mark. So is 'all' option okay when positions of each of the atoms
of TiO2 crystal (2160 atoms total) are restrained in space? Apparently, it
does not seem correct, since positions of the atoms of TiO2 crystal change
when 'all' option is applied. However, it does not give error as 'com'
opti
On Mon, Mar 24, 2014 at 4:44 PM, Chetan Mahajan wrote:
> Hi Mark,
>
> I am restraining positions of each of the atoms of TiO2 crystal. Could you
> comment again why should simulation crash when 'com' option is used against
> 'all' option?
Don't know, I'd have to read the code, and I don't care e
Hi Mark,
I am restraining positions of each of the atoms of TiO2 crystal. Could you
comment again why should simulation crash when 'com' option is used against
'all' option? Also, description in the manual does not answer my question:
when is 'all' option generally used? When is 'com' option gener
The segmentation fault is highly unusual, and suggests that the
installation of gromacs used a shared library that has now
migrated/changed/whatever. I suggest you discuss that with your system
admins and ask them to re-install, or re-run the GROMACS regression tests,
to check things are OK.
Mark
On 3/24/14, 8:52 AM, MUSYOKA THOMMAS wrote:
Hello. I have a protein pdb and the best pose of a ligand obtained through
docking using auto dock. However, when I combine the ligand and protein
using the discovery studio, some residues like Lysine in the protein pdb
gets protonated as well as the
Hi Justin,
Thank you very much for your reply. I shall try to work my way around and
see.
Kind regards,
Ankita
On Mon, Mar 24, 2014 at 12:12 PM, Justin Lemkul wrote:
>
>
> On 3/24/14, 7:57 AM, Ankita Naithani wrote:
>
>> Hi, so I modified my mdp file which now looks like the following:
>>
>
Hello. I have a protein pdb and the best pose of a ligand obtained through
docking using auto dock. However, when I combine the ligand and protein
using the discovery studio, some residues like Lysine in the protein pdb
gets protonated as well as the N-terminal residue. Is this unusual and can
it a
No, semicolons start comments, not end lines
On Mar 24, 2014 1:07 PM, "Pavan Kumar" wrote:
> It might be some typographical errors.
> Check the mdp file thoroughly. I think semicolon is required for the last
> line in your mdp file
>
>
> On Mon, Mar 24, 2014 at 5:18 PM, Ankita Naithani
> wrote:
>
On 3/24/14, 7:57 AM, Ankita Naithani wrote:
Hi, so I modified my mdp file which now looks like the following:
title= production MD
; Run parameters
integrator= md; leap-frog algorithm
;nsteps= 2000; 0.005 * 2000 = 10 ps or 100 ns
;nsteps= 200
On 3/24/14, 7:56 AM, Pavan Kumar wrote:
It might be some typographical errors.
Check the mdp file thoroughly. I think semicolon is required for the last
line in your mdp file
Semicolons are never required; they're comments and are ignored by grompp.
-Justin
On Mon, Mar 24, 2014 at 5:18 P
On 3/24/14, 7:48 AM, Ankita Naithani wrote:
Hi Pavan,
Thank you for your response. I am trying to generate the tpr file with the
following parameter;
; Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 25 fs
rlist= 1.0
On Mon, Mar 24, 2014 at 12:48 PM, Ankita Naithani
wrote:
> Hi Pavan,
> Thank you for your response. I am trying to generate the tpr file with the
> following parameter;
> ; Neighborsearching
> ns_type= grid; search neighboring grid cells
> nstlist= 5; 25 fs
> rli
On Mon, Mar 24, 2014 at 12:17 PM, Ankita Naithani
wrote:
> Hi,
>
> I am trying to run a simulation of my protein (monomer ~500 residues). I
> had few questions and erors regarding the same.
> I have previously run the simulation of the apo form of the same protein
> using Gromacs 4.5.5 which was a
Hi, so I modified my mdp file which now looks like the following:
title= production MD
; Run parameters
integrator= md; leap-frog algorithm
;nsteps= 2000; 0.005 * 2000 = 10 ps or 100 ns
;nsteps= 20; 0.005 * 20 = 1 ns
;dt= 0.00
It might be some typographical errors.
Check the mdp file thoroughly. I think semicolon is required for the last
line in your mdp file
On Mon, Mar 24, 2014 at 5:18 PM, Ankita Naithani
wrote:
> Hi Pavan,
> Thank you for your response. I am trying to generate the tpr file with the
> following para
Hi Pavan,
Thank you for your response. I am trying to generate the tpr file with the
following parameter;
; Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 25 fs
rlist= 1.0; short-range neighborlist cutoff (in nm)
rcoulo
Hello Ankita
You have to just include the following line in your mdp file
cutoff-scheme=Verlet
And run your grompp with the modfied mdp file to generate tpr file and then
mdrun.
Hope this doesn't give you the same error
On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani
wrote:
> Hi,
>
> I am tryin
Hi,
I am trying to run a simulation of my protein (monomer ~500 residues). I
had few questions and erors regarding the same.
I have previously run the simulation of the apo form of the same protein
using Gromacs 4.5.5 which was available at the cluster facility I was using
and also which is instal
I can't delete a post. This is a mailing list, not a forum (even if you are
reading on some half-broken nabble setup, or something).
A plain
cmake ..
from an empty build tree is designed to just work if you then run mdrun on
the same machine. If it doesn't, that's an error we want to fix, but as
On 3/24/14, 5:33 AM, Satyadeep Roat wrote:
I want to make a new itp file and add two atoms in it.
Something like this
;[atoms]
1a1 q r1
2 a2 -q r2
Close, but not correct. The format for [atoms] is listed in manual section
5.7.2. There
On 3/24/14, 5:32 AM, ooker wrote:
@Mark Abraham: I have received your email but because I don't see it on the
thread so I think you deleted your answer. Sorry about that. I'm still new
with the mail list. Anyway, I have already deleted the build folder and
make a fresh install but it doesn't so
I want to make a new itp file and add two atoms in it.
Something like this
;[atoms]
1a1 q r1
2 a2 -q r2
On Mon, Mar 24, 2014 at 2:47 PM, Mark Abraham wrote:
> I don't understand your description.
>
> Mark
> On Mar 24, 2014 4:09 AM, "deep" wr
Thank you Justin.
This is what I have tried, but obviously gone wrong with [settles]. I'll try
again.
V
--
View this message in context:
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Sent from the GROMACS Users Forum mailing list ar
@Mark Abraham: I have received your email but because I don't see it on the
thread so I think you deleted your answer. Sorry about that. I'm still new
with the mail list. Anyway, I have already deleted the build folder and
make a fresh install but it doesn't solve.
@Justin Lemkul: my machine is In
Amber forcefields use terminal residues that are parametrized differently
from normal ones. You can't just label a few atoms as the terminal ones and
have it work; you need a whole residue, and this makes a single-residue
zwitterion topology impossible to build with pdb2gmx. You need to cap the
te
I don't understand your description.
Mark
On Mar 24, 2014 4:09 AM, "deep" wrote:
> I want to create a polarizable particle system consisting of a sphere
> carying
> charge q and some size r1 on which a oppositively charge -q is present with
> some other size r2 . Overall I want to create a collo
On Mar 24, 2014 1:10 AM, "Chetan Mahajan" wrote:
>
> Dear all:
>
> I am trying to get a simulation of water solvated titanium oxide running.
> When 'all' option is used for refcoord-scaling, simulation runs ok.
> However, when 'com' option is used for refcoord-scaling, simulation
crashes
> with an
Dear People,
I am trying to simulate glycine molecule using amber ff. I have changed the
residues in pdb file with N and C respectively.
ATOM 1 NNGLY1 -1.476 0.232 0.252 1.00 0.00
ATOM 2 CA CGLY1 -0.012 0.296 0.348 1.00 0.00
ATOM 3 CCGLY
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