sir,
I have a basic doubt about remd simulation. In remd is it possible to
run 16 replicas in 8 processors?
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Dear GMX Users,
I am wish to perform a conformational transition simulation using
coarse-grained models (SBM http://smog-server.org/). I wanted to apply flooding
to explore the conformational transition and have open-close transition my
trajectory. But what I find is that when I start from a o
Dear Gromacs users,
Please somebody help .
editconf computs the incorrect value of "mass of input". I tried to resolve
this problem but failed. Previously I was doing AOt but now I just found that
the molecule OS1 =O2L showing error . Here I posted my A.pdb, RM.rtp
atomtypes.atp. The mass of
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Hi,
Please tell me what is wrong in my input file. I am not getting APL
along with std deviation values.
Following is the input and output for calculating APL
Input file
coord_file md.gro
file_type gro
num_frames1
num_lipid_types 1
resname1
Dear gmx-users,
We intend to perform free energy calculations by pulling a polypeptide
along water-hexane interface. We need to pull the polypypeptide from the
water layer towards the hexane layer (crossing the interface). For this we
position restrained one hexane molecule in the bulk of hexane (
On 9/30/13 5:19 AM, suhani nagpal wrote:
Greetings
I have a large protein of 303 residues and one of the lysine is acetylated
in the same.
The forcefield selection according to the options says as follows:
Residue 'ALY' not found in residue topology database
For more information and tips for
Greetings
I have a large protein of 303 residues and one of the lysine is acetylated
in the same.
The forcefield selection according to the options says as follows:
Residue 'ALY' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
we
On 9/14/13 7:31 AM, mabbasi wrote:
Dear All users
I used OPLS ff for my system.
After md production I get this error:
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated.
http://www.gromacs.org/Docum
Dear All users
I used OPLS ff for my system.
After md production I get this error:
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated.
maryam abbasi, PhD student of Medicinal Chemistry
Department of Med
On 9/3/13 7:20 AM, Prajisha Sujaya wrote:
Respected sir,
I am facing a problem while simulating the tRNA molecule
while converting pdb to gro,
Fatal error:
Atom OP3 in residue A 1 was not found in rtp entry RA5 with 31 atoms
while sorting atoms.
force field used 3 (AMBER96 prot
Respected sir,
I am facing a problem while simulating the tRNA molecule
while converting pdb to gro,
Fatal error:
Atom OP3 in residue A 1 was not found in rtp entry RA5 with 31 atoms
while sorting atoms.
force field used 3 (AMBER96 protein, nucleic AMBER94), water model TIP3P.
kind
>In an implicit, non-periodic system, it is more likely that the ligand
will
>float away from the protein. I've tried it and that's all that ever
happens.
>Moreover, the current Gromacs version does not support implicit solvent on
GPU
>and the previous version that did had very limited functionali
hi
please help me
must all mdp files to be similar for g_lie program? shouldn't i use of PME in
all mdp files?
what edr file must i use as input file for g_lie?
best regards
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On 6/20/13 11:11 PM, Hari Pandey wrote:
Hi all gromacs users
I have following (NVT.mdp) (NPT.mdp) and (NVE.mdp) . I have three parts of
system, A, B and C.
I want to put thermostat on A and C and couple the tempereture and do not put
any thermostat on B.
What I want is: after some ps,
Hi all gromacs users
I have following (NVT.mdp) (NPT.mdp) and (NVE.mdp) . I have three parts of
system, A, B and C.
I want to put thermostat on A and C and couple the tempereture and do not put
any thermostat on B.
What I want is: after some ps, temperature of A and C should be constant (
http://1515-org.com/njpczvkv/uvjeyddwjvclsn.php
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On 2013-06-01 02:24, Marcelo Vanean wrote:
> Hello to everyone. In version 4.5.5, calculating the viscosity with the
> command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and
> visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a
> value of zero for viscosity usi
Dear Sir,
In pulling simulations how to set pull_rate and
pull_k .On which basis we can set these values.
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Dear all.I want to study Diffusion coefficient of carbonmonoxide in water...I
get different values of force constant partial charge while searching for those
constants. Can anyone help me providing the values of partial charge (of CO),
force constant and lennard jones parameter used in the simul
Sir,
I want to do pulling simulations for membrane protein and gold
nanoparticles. Can you please suggest me some tutorials for calculating
youngs modules ,stress and strain.
Thank You
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I want to do simulation of protein at pH 12 so i have to deprotanate
tyrosine,tryphtophan.Can you please tell me how i can do with pdb2gmx
command
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I really don't think thats possible at the moment. All interactions in Reax, if
I recall correctly, are dependent on bond order, which is not an implemented
concept in gromacs.
Erik
On 6 May 2013, at 12:51, Sathish Kumar wrote:
> hai
> i would like to use Reax force field,can we use r
I want to do simulation of protein at pH 12, in this case experimentally
reported that the disulphide bonds of protein was broken and sulphurs
become S negative . Can you please tell me making of disulphide as S- and
S- is it correct and how to set force field to this.
hai
i would like to use Reax force field,can we use reax force field
in gromacs and if any one please tell to me weather reax ff is useful for
protein
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On 5/5/13 5:10 AM, Group Gro wrote:
Dear GROMACS users,
I am working on protein-ligand complexes and when I run "mdrun -deffnm nvt.tpr
-v" I run into this error:
Fatal error:
2 particles communicated to PME node 1 are more than 2/3 times the cut-off out
of the domain decomposition cell of th
Dear GROMACS users,
I am working on protein-ligand complexes and when I run "mdrun -deffnm nvt.tpr
-v" I run into this error:
Fatal error:
2 particles communicated to PME node 1 are more than 2/3 times the cut-off out
of the domain decomposition cell of their charge group in dimension x.
I foun
On Wed, Apr 10, 2013 at 3:49 PM, Liron Cohen wrote:
> hi,
>
> i am using gromacs 4.5 and i am trying to run an energy minimization and
> then temperature equilibration for a system of two charged plates plates
> solvented in water.
> the plates are made of fake atoms which has carbon atoms paramet
hi,
i am using gromacs 4.5 and i am trying to run an energy minimization and then
temperature equilibration for a system of two charged plates plates solvented
in water.
the plates are made of fake atoms which has carbon atoms parameters, and a bond
length of 0.2 nm.
the plates are made from o
Dear All
I have done the lysozyme tutorial and at the end of the simulation a .gro file
have
been produced. would you please tell me whether this gro file contains the
structure
of our molecules at the end of simulation or not? I mean does it show the
simulation
box at the end of simulation?
Hai
I have done 10ns simulation for a protein to this i want to
calculate DCCM map.can you please suggest me how to calculate this map.
Thank You.
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plain what you are trying to do in detail to get
>> more productive help.
>>
>> Cheers,
>> EB
>>
>> -----Original Message-
>> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
>> On Behalf Of Yongliang Yang
>> Sen
more
productive help.
Cheers,
EB
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Yongliang Yang
Sent: Monday, 25 March 2013 5:01 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] (no subject)
Dear EB,
Many thanks for the kind
more
productive help.
Cheers,
EB
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Yongliang Yang
Sent: Monday, 25 March 2013 5:01 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] (no subject)
Dear EB,
Many thanks for the kind
Dear EB,
Many thanks for the kind reply! We have revised the improper section
followed your advice. The force field is amber99sb. Unfortunately, the
program complained again, "No default proper dih. types'. Any advice?
Thanks!
Cheers
Jeremy
---
Hi Jeremy,
I have checked how impro
On 1/9/13 8:57 AM, sara azhari wrote:
Dear Justin
first ,I get error on atom number .
after change emtol to 10 , I get same error on atom number .
what' your idea? how to solve it?
mdrun probably did a different number of steps and/or moved through
configurations different.
Dear Justin
first ,I get error on atom number .
after change emtol to 10 , I get same error on atom number .
what' your idea? how to solve it?
I use this file for PR step , but I get this error:
A charge group moved too far between two domain decomposition
your system mig
On 1/6/13 7:29 AM, fatemeh ramezani wrote:
I didn't set epsilon and sigma between au and other atoms equal to zero, but I
have not enteredanyEpsilon and Sigmafor them , and once again I set them zero
and try it again.
If you didn't set them at all, grompp should have given a fatal error.
I didn't set epsilon and sigma between au and other atoms equal to zero, but I
have not enteredanyEpsilon and Sigmafor them , and once again I set them zero
and try it again.
But if closing of gold to protein, is because of charge, how do I delete its
effect ? How can I uncharged the system?
On 12/17/12 12:53 PM, Shine A wrote:
sir,
I am studying dynamics of a membrane protein using oplsaa force field.
Energy minimization during nvt equilibration getting error like this.
Fatal error:
1 particles communicated to PME node 1 are more than 2/3 times the cut-off
out of the doma
sir,
I am studying dynamics of a membrane protein using oplsaa force field.
Energy minimization during nvt equilibration getting error like this.
Fatal error:
1 particles communicated to PME node 1 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group
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Hi friends,
I'm interested in using Thole type model for water (polarizable) TTM2
J. Phys. Chem. A, 2006, 110 (11), pp 4100 or TTM3 ;J. Chem. Phys. 128,
074506 (2008) ) model.
Can someone send me itp file for water..
Thanks
Ananya
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Dear all,
When I try to install gromacs-4.5.5 on my centos system, I meet trouble. I
installed fftw-3.3.2 and then install gromacs-4.5.5. When I type /.configure
command, I got the error information:
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-g
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On 10/3/12 5:17 PM, Ho, Tuan A. wrote:
Dear Gromacs users,
I would like to simulate water on Ruthenium surface. Would you please suggest
the force field used to describe Ru.
You're not likely to find one built into Gromacs by default.
http://www.gromacs.org/Documentation/How-tos/Parameteriz
Dear Gromacs users,
I would like to simulate water on Ruthenium surface. Would you please suggest
the force field used to describe Ru.
Many thanks.
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Dear gmx users
I am analyzing simulation results of a system including carbon
nanotube+surfactant molecules.
I would like to calculate the number of surfactants located on a
specific distance(say 1 nm ) from nanotube in each timestep or average
of that quantity.I would be really appreciated if
some
On 8/28/12 1:25 PM, Lingyun Wang wrote:
Hi all,
I want to model a protein on the surface of a bilayer membrane. Is it
reasonable to add less water molecules to the bilayer side without protein? Or
the water should be the same on both side of membrane? Thanks.
Given periodic boundaries con
Hi all,
I want to model a protein on the surface of a bilayer membrane. Is it
reasonable to add less water molecules to the bilayer side without protein? Or
the water should be the same on both side of membrane? Thanks.
Lingyun
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On 8/2/12 10:09 AM, vidhya sankar wrote:
Dear Gromacs user , I Write Some linux .sh programming to automate
grompp and mdrun process in Clustering which is as Follows
Could Any one of you point out the error in following script files ? is it
correct or not.
Are you getting an
Dear Gromacs user , I Write Some linux .sh programming to automate
grompp and mdrun process in Clustering which is as Follows
Could Any one of you point out the error in following script files ? is it
correct or not.
#!/bin/bash
#! -l nodes=1:ppn=4
# load the modules
# preproc
s
Dear gmx-users
I am trying to calculate the optical rotation of a molecule in solution. There
are several examples of this in the literature where they take snapshots of
molecule at intervals throughout the trajectory, calculate optical rotation,
and average them to get a solvated optical rotat
Dear Sir,
Thanks sir.
I am using the ffG43a1 force field. Mine is an unusual unusual peptide and got
the necessary files from prodrg server.
and also pasting the top file. Please tell where , m making the mistake.
The Force Fields to be included
#include "ffG43a1.itp"
; Include nmab2 topology
#
On 7/14/12 3:34 AM, sara elham wrote:
Dear Gromacs users
I want to find the solution for my problem from mailing list, but it
give me this massage:
"Timeout expired. The timeout period elapsed prior to completion of
the operation or the server is not responding."
The website experiences inte
Dear Gromacs users
I want to find the solution for my problem from mailing list, but it
give me this massage:
"Timeout expired. The timeout period elapsed prior to completion of
the operation or the server is not responding."
I tried to registration again, but in the section " Type the
characters
>g_energy -dp IIRC.
>g_energy -h is your friend. By the way in single precision you have 7-8 digits
>only.
It seems that the X.edr file only contains 6 digits (if mdrun was done
with single precision).
So g_energy -f X.edr -dp gives me only 6 digits.
To wish list: X.edr file should contain as ma
On 7/11/12 6:19 AM, amir abbasi wrote:
Thanks Justin,
But I want to neutralize my system in implicit solvent.
In Amber I had use Debye screening but in gromacs I don't know what should I do.
From my understanding, this remains an unresolved issue.
-Justin
On Wed, Jul 11, 2012 at 2:45 PM,
Thanks Justin,
But I want to neutralize my system in implicit solvent.
In Amber I had use Debye screening but in gromacs I don't know what should I do.
On Wed, Jul 11, 2012 at 2:45 PM, Justin A. Lemkul wrote:
>
>
> On 7/11/12 6:00 AM, amir abbasi wrote:
>>
>> Hi All!
>> I want to use Implicit so
On 7/11/12 6:00 AM, amir abbasi wrote:
Hi All!
I want to use Implicit solvent to simulate a nucleic acid sequence.
How can I do it?
I use this command:
genion -s ions.tpr -o nucleic_ions.gro -p nucleic.top -pname K+ -nname
CL -neutral -conc 0.1
ions.tpr file is same as umbrella sampling tutori
Hi All!
I want to use Implicit solvent to simulate a nucleic acid sequence.
How can I do it?
I use this command:
genion -s ions.tpr -o nucleic_ions.gro -p nucleic.top -pname K+ -nname
CL -neutral -conc 0.1
ions.tpr file is same as umbrella sampling tutorial.
I got this error message:
Fatal error:
Dear Gromacs Users,
I have a system consists of cyclohexan, pentanol, surfactant and water
in MARTINI coarse-grained ff, when I do pr.mdp for this system
(posre.itp file is only for surfactant), water molecules are not
distributed and are aggregated in one place in the box.
I don't know what shoul
On 6/19/12 8:58 AM, ankita oindrila wrote:
I am doing simulation of membrane protein in lipid bilayer for my
college project!.
After making the complex of protein and lipid bilayer, I was going
to the step using genbox to solvate the system.
The error that i am now getting is :
Fat
I am doing simulation of membrane protein in lipid bilayer for my
college project!.
After making the complex of protein and lipid bilayer, I was going
to the step using genbox to solvate the system.
The error that i am now getting is :
Fatal error:
Not enough memory. Failed to realloc 10
On 6/18/12 4:55 AM, ankita oindrila wrote:
i am doing protein in bilipid membrane simulation.
while packing the protein in the lipid membrane step, i am getting this error.
command : perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro
5 area.dat
Reading.
Scaling lipids
Ther
i am doing protein in bilipid membrane simulation.
while packing the protein in the lipid membrane step, i am getting this error.
command : perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro
5 area.dat
Reading.
Scaling lipids
There are 0 lipids...
Illegal division by zero at i
On 6/13/12 5:09 AM, Seera Suryanarayana wrote:
Dear all gromacs users,
I am doing moleculer dynamics by using gromacs software.I
got the following error after using the commond" mdrun -deffnm nvt".
Fatal error:
A charge group moved too far between two domain decompositio
Dear all gromacs users,
I am doing moleculer dynamics by using gromacs
software.I got the following error after using the commond" mdrun -deffnm
nvt".
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not w
On 12/06/2012 3:18 PM, tarak karmakar wrote:
Dear All ,
I am facing problem in matching the coordinates number in this two
files, em.gro and toplogy.top.
I have tried with changing the number of solvents, adding ions (Na+)
but in vain
_Note :: My system has ' -1.00 ' charge ...so I
Could you paste your .top file and the command your add ions? Maybe the Cl-
ion was also added when you added Na+ ion?
On Tue, Jun 12, 2012 at 1:18 PM, tarak karmakar wrote:
> Dear All ,
>
> I am facing problem in matching the coordinates number in this two files,
> em.gro and toplogy.top.
> I ha
Dear All ,
I am facing problem in matching the coordinates number in this two files,
em.gro and toplogy.top.
I have tried with changing the number of solvents, adding ions (Na+)
but in vain
*Note :: My system has ' -1.00 ' charge ...so I have added one Sodium
ion*
So can anyone please g
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On 5/31/12 7:37 AM, Subramaniam Boopathi wrote:
how to assign charge and charge group number when new residue as being added to
the existing amino acid rtp file
The details depend on the force field you're using.
http://www.gromacs.org/Documentation/How-tos/Parameterization
-Justin
--
===
On 31/05/2012 9:37 PM, Subramaniam Boopathi wrote:
how to assign charge and charge group number when new residue as being
added to the existing amino acid rtp file
Read about the file format in the manual.
Mark
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how to assign charge and charge group number when new residue as being
added to the existing amino acid rtp file
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On 5/16/12 8:49 AM, rama david wrote:
Hi Gromacs Friends,
I plan to simulate protein In Trifluoro Ethanol solvent
using G96 53a6 FF
Please help to define parameters in md.mdp
For water I am using following mdp file
lincs_order= 4; also related to accuracy
; Neighborsearchi
Hi Gromacs Friends,
I plan to simulate protein In Trifluoro Ethanol solvent
using G96 53a6 FF
Please help to define parameters in md.mdp
For water I am using following mdp file
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search n
Hi Guys
I was using the program http://q4md-forcefieldtools.org/RED/ to derrive ESP
based charges for some molecules that I study using OPLSAA force field. Is this
a correct method to do so if not please let me know what are the other
methods that are available.
thanks alot
Milinda Samarawee
Dear Justin
I really appreciate for your reply.
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Hello,
I am doing solvation dynamics for my system.
I have system with diatomic (PA---NE)solute surrounded by water molecules.
I am running simulation for two differcent cases.
1. PA charge=0 and NE charge=0 : No charge on solute
2. PA charge=+1 and NE charge=-1 : Charge on solute
For seco
Rev0Iuti0n - h0me business
http://transcom68.com/httpckhatcpa12k2.php?pesIDid=318
Wed, 4 Apr 2012 4:31:32
__
" Peter Wilks lives? they givea glance at one another, and nodded their heads,
as much as to say, Whatd I tell you? Then one of them says, kind of soft and
gentl
Dear Gromacs users,
I am performing MD simulation of an 14 units oligosaccharide on Gromacs
4.5.4. I am able to successfully do a 10 ns simulation on a DELL-precision
workstation and also a 5ns simulation on tyrone cluster using a PBS script
(shown below). However, when I am trying to proceed for
Anik Sen wrote:
Respected Sir,
I am new to gromacs. Am using GROMACS 4.5.5
version. I have two questions..
1. I want to know about plotting the co-ordination number (CN) of the
water molecules around one of my substrate say a KCl molecule for
example. What should
Respected Sir,
I am new to gromacs. Am using GROMACS 4.5.5 version. I
have two questions..
1. I want to know about plotting the co-ordination number (CN) of the water
molecules around one of my substrate say a KCl molecule for example. What
should i do to get the CN num
Hi
Thanks alot.
With your suggestions my problem was solved.
Saly
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saly jackson wrote:
Hi,
I want to add 8 of a molecule including 6 atoms. But when I run each
of the following commands I
System total charge: 0.000
Grid: 5 x 5 x 5 cells
nri = 1948, nrj = 22927
Try 63309box_margin = 3t overlap:
Neighborsearching with a cut-off of 3
Table routines are us
Hi,
I want to add 8 of a molecule including 6 atoms. But when I run each of
the following commands I
System total charge: 0.000
Grid: 5 x 5 x 5 cells
nri = 1948, nrj = 22927
Try 63309box_margin = 3t overlap:
Neighborsearching with a cut-off of 3
Table routines are used for coulomb: FALSE
Tabl
Dear Gromacs users!
I want to simulate membrane receptor in the Gromos 56 force field in the
vacuu and I have some methodological questions.
1- I need to edit topology of my structure by adding one DOUBLE covalent
bond between desires atoms ( they have been already placed in the desired
adjacen
The following is a part of the dna pdb file, which I am using:
ATOM 1 OH DG5 X 1 13.663 36.760 21.465 0.00 0.00
ATOM 2 CT DG5 X 1 14.791 36.040 21.150 0.00 0.00
ATOM 3 CT DG5 X 1 14.771 34.703 21.873 0.00 0.00
ATOM 4 OS DG5 X 1 16
Yoshus Kumka wrote:
Hello,
I am trying to a simple energy minimization with my DNA molecule I
created with 3DNA program. Below is a snippet of a pdb file where I've
only included coordinates for one residue to save space (/Actual file
contains coordinates for 12-mer DNA/).
So my question
Hello,
I am trying to a simple energy minimization with my DNA
molecule I created with 3DNA program. Below is a snippet of a pdb file where
I've only included coordinates for one residue to save space (Actual file
contains coordinates for 12-mer DNA).
So my question is why is t
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Hi all,
I am new to the Gromacs and just started to use Gromacs for MD simulations.
I am tring to extend the simulation (protein in a box) 10 ns more. For
this, I used the following command:
grompp -f md.mdp -c md_first.gro -t md_first.cpt -p topol.top -o
md_second.tpr
mdrun &
It seems to run..
I a
On 12/01/2012 5:44 PM, Anik Sen wrote:
fftw-3.3 installation:
first gone to the fftw3.3 folder
./configure --enable-threads --enable-float --enable-sse
--enable-shared --prefix /home/ganguly/Gromacs/fftw3.3
.
.
.
make
.
.
.
make install
Then gromacs 4.5.5 is being installed.
installation:
fir
y@localhost gromacs-4.5.5]$
________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Javier Cerezo [j...@um.es]
Sent: Wednesday, January 11, 2012 5:12 PM
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] (no subject)
You need to post how
:* Re: [gmx-users] (no subject)
Hi
You should compile your fftw with --enable-shared if you want to link
your gromacs installation to shared libraries (which is the default in
the latest versions). Check the installation instructions in the website.
Javier
El 11/01/12 08:20, Anik Sen escribió
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