On 9/15/14 10:29 AM, Despoina Tzeli wrote:
Hi to everyone! I want to run a simulation using gromos53a6 force field, but i
cannot find
some angle definitions (ga_) or their values! These are :
1) CH3 - C - CH3
2) C - O - C
3) O - C - N
4) N - CH - C
Does anybody know them?Where can I get
On 9/15/14 3:12 PM, shahab shariati wrote:
Dear Justin
Thanks for your answer.
You said The raw output of g_traj in this case is not very useful
I want to know position and location of drug molecules relative to the DPPC
bilayer during simulation time.
In your opinion, how should I use
On 9/16/14 1:04 PM, LIPSCOMB, THOMAS wrote:
?Dear Gromacs mailing list,
I need to know if your program can simulate protein-membrane interactions as
this website claims:
http://www3.mpibpc.mpg.de/groups/de_groot/compbio1/p5/index.html#contents
If it can then please help me use Gromacs to
On 9/16/14 4:48 AM, Kester Wong wrote:
Dear gromacs team,
I have recently converted a TIPS3P system (10k molecules) to a SWM4-NDP model.
As I followed the instruction as listed below, I find it hard for beginners like
me to convert the water structure:
On 9/16/14 1:43 PM, Dawid das wrote:
Dear gromacs experts,
I'd like to obtain coordinates of a group of atoms from trajectory file.
What I mean is simply get an output file with coordinates for each atom and
for each frame.
Is it possible to do that?
Yes. Use g_traj with a suitable index
On 9/16/14 9:15 PM, Kester Wong wrote:
Dear Justin,
Thank you for the feedback. Yep, the converted structure is not any better than
a starting configuration, i.e. discontinued ensemble velocitites and another
energy minimisation for the converted structure is necessary.
What I thought would
On 9/17/14 7:01 AM, h.aliza...@znu.ac.ir wrote:
Dear GROMACS users,
Is it possible to track H-bonding or distance between two certain atoms in
GROMACS?
Of course. See Chapter 8 for available analysis tools. There are several
designed to do exactly what you want.
-Justin
--
On 9/17/14 7:20 AM, Anurag Dobhal wrote:
I am getting an error while running the commmand
gmx grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
Fatal error:
Unknown bond_atomtype MNH3
That shouldn't happen unless you erroneously delete the MNH3 definition within
On 9/18/14 8:01 AM, Kester Wong wrote:
Dear gromacs users,
Has anyone experienced a problem with running polarisable water model SWM4-NDP
with the following warning: Shell particles are not implemented with domain
decomposition?
Out of curiosity, what is the source of your SWM4-NDP
On 9/18/14 6:38 AM, RINU KHATTRI wrote:
hello
i am also facing the same problem i worked on the protein complex
(popc ) but once again i am using same procedure its gives error even
i changed .mdp file parameters
Changed to what? From what?
after running it gives 61%
mdrun
grompp -f
On 9/18/14 4:53 AM, Ujwala Patil wrote:
Hello I am doing simulation of dioxane+ water system
during energy minimization i got error
Too many LINCS warnings (1337)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable
On 9/18/14 4:42 AM, Sathish Kumar wrote:
Hai
I run the umbrella sampling with the help of tutorial of
justinIn my system rna is binding with gold nanoparticle...to find out
the binding energy i run the umbrella sampling using the space 0.2 nm and i
got total 59 configurations, each
On 9/17/14 10:07 PM, Kester Wong wrote:
That would be great Justin, I look forward to using the new Drude tool.
I have registered but could not upload a file to the User Contribution page.
See the note on the homepage about getting permission to modify pages:
http://www.gromacs.org/
On 9/17/14 6:54 PM, Yunlong Liu wrote:
Hi,
I am trying to use Gromacs 5.0 to run membrane protein simulation. I built my
membrane protein system with POPC membrane and TIP3P water in VMD. Then I used
gmx pdb2gmx to build gromacs topology files.
My force field is charmm22* and it contains
On 9/17/14 6:02 PM, Dallas Warren wrote:
Can I put in a request to have the full list of GROMACS commands/scripts, along
with their help text, added back to the end of the manual? Or at least have a
separate PDF available?
What was the reason for removing that section?
Over the years I
On 9/18/14 11:51 AM, pratibha kapoor wrote:
Hi users
I have question regarding difference between pbc whole and pbc nojump
options using trjconv. Please help me understand this.
Have you read trjconv -h yet?
-Justin
--
==
Justin A. Lemkul,
On 9/18/14 2:04 PM, Carlos Navarro Retamal wrote:
Dear gromacs users,
In order to measure the interactions between a Protein with respect to a
mixture solvent solution (glycerol-water) i’m trying to measure the RDF
between the protein with respect to the C and O atoms of Glycerol
gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Justin Lemkul
jalem...@vt.edu
发送时间: 2014年9月18日 20:30
收件人: gmx-us...@gromacs.org
主题: Re: [gmx-users] membrane protein simulation - errors
On 9/17/14 6:54 PM, Yunlong Liu wrote:
Hi,
I am trying to use Gromacs 5.0 to run membrane protein simulation. I
On 9/18/14 1:11 PM, David van der Spoel wrote:
On 2014-09-18 14:26, Justin Lemkul wrote:
On 9/18/14 8:01 AM, Kester Wong wrote:
Dear gromacs users,
Has anyone experienced a problem with running polarisable water model
SWM4-NDP
with the following warning: Shell particles
On 9/18/14 4:45 PM, Carlos Navarro Retamal wrote:
Hi Justin,
First of all thanks for your reply.
It worked, but i’m getting weird results.
When i measured the RDF between:
Protein (COM) - Glycerol (the entire molecule) i got a huge pick at 0.022 nm,
which doesn’t make any sense (because i
On 9/19/14 8:43 AM, gromacs query wrote:
Hi All
I have some pdb file and I removed hydrogens. When I try to make ndx file
using some residue option then rather printing atom numbers in that residue
it prints line number where that residue starts and ends.
make_ndx -f no_H.pdb -o test.ndx
On 9/19/14 5:15 PM, gromacs query wrote:
Hi Justin
Hope it makes sense now :) Here is the link (small piece of some pdb
without hydrogens)
http://s000.tinyupload.com/?file_id=09348261523279878452
http://s000.tinyupload.com/index.php?file_id=09348261523279878452
I used this command: (note
Teléfono: 56-71-201 798,
Fax: 56-71-201 561
Email: carlos.navarr...@gmail.com or cnava...@utalca.cl
On Friday, September 19, 2014 at 5:35 PM, Justin Lemkul wrote:
On 9/18/14 4:45 PM, Carlos Navarro Retamal wrote:
Hi Justin,
First of all thanks for your reply.
It worked, but i’m getting weird
On 9/19/14 6:07 PM, Carlos Navarro Retamal wrote:
Hi Justin,
Thanks again for all your help.
If the problem is related to periodicity, why if i consider the whole protein i
got ‘normal’ results?
A normal (non-COM-based) RDF is an atom-based RDF, so periodicity doesn't affect
the outcome.
On 9/22/14 4:48 AM, Anurag Dobhal wrote:
I am getting an error while running the commmand
gmx grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
Fatal error:
Unknown atomtype OW
please help !!!
You deleted a necessary atom type. Follow the instructions carefully and
On 9/22/14 8:46 AM, marcello cammarata wrote:
Hi,
i had checked all the archives, i have read about 100posts in the last 2
month.
Nobody have problem similar to mine.
Problem for me are Two.
1- instead i am a doctor, i am not able to find the right advice at your site.
2- In your site
On 9/22/14 3:00 AM, Anurag Dobhal wrote:
I have followed the following steps for installaing gromacs 5.0.1
tar xfz gromacs-5.0.1.tar.gz
cd gromacs-5.0.1
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source
.
-Justin
On Thu, Sep 18, 2014 at 5:58 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/18/14 6:38 AM, RINU KHATTRI wrote:
hello
i am also facing the same problem i worked on the protein complex
(popc ) but once again i am using same procedure its gives error even
i changed .mdp file parameters
On 9/22/14 10:14 AM, Yaser Hosseini wrote:
hi guys i have a problems with gromacs command .how can i can solve
this problems:
i install gromacs and i dont know what can i do:
gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
No command 'gmx' found, did you mean:
On 9/22/14 10:45 AM, Александр Селютин wrote:
Thanks to everyone
I have idea that I can stop simulation, change topology(move end of
molecule, add new atoms) and start again. It should be repeated every 2 ps.
But it can be very slowly. Does anybody know how to do it more correctly?
I don't
On 9/22/14 2:26 PM, Anu Chandran wrote:
Dear all,
I have carried out simulations of two homologous proteins (~38kDA) using
Gromacs v4.5.3 using OPLS force field. The protein consists of three
domains. Structural studies using cystallography reported earlier showed
that the two proteins differ
On 9/23/14 7:36 AM, h.aliza...@znu.ac.ir wrote:
Dear users,
Can we calculate electrostatic energy between two groups of atoms in
GROMACS?
energygrps in the .mdp file.
Whether or not that quantity means anything (if using PME, for instance) is
another matter and depends to some extent on
On 9/23/14 12:45 PM, Johnny Lu wrote:
Hi.
On stampede of xsede.org https://portal.xsede.org/tacc-stampede, I
compiled cmake, and then gromacs 4.6.7 with and without gpu, with the
following cmake configuration:
without gpu:
module load mkl
module load cuda/6.0
module load mvapich2
export
On 9/23/14 1:18 PM, ABEL Stephane 175950 wrote:
Hello all,
I am trying to convert some GLYCAM parameters to do simulations with the
GROMACS code. In the glycam force field, several dihedral terms have negative
barrier height values, for instance, -20 in the following parameter:
On 9/23/14 7:43 PM, marcello cammarata wrote:
Do you know how change force field?
how i can do this?
Everything you need to create the polymer is described here:
http://www.gromacs.org/Documentation/How-tos/Polymers
The page includes a link to a discussion that goes step-by-step through
On 9/25/14 1:42 AM, Batdorj Batsaikhan wrote:
Dear gmx users,
Can I calculate free energy of Tutorial 1 of Justin's tutorials?
Free energy of what? The system? I doubt you could ever get a reliable
estimate of that. The free energy code in Gromacs is set up to measure free
energy
On 9/25/14 4:57 AM, marcello cammarata wrote:
Hi to all,
in order to find the position tangled of a polymer chain,
i tried to follow the indication of hte page Polymer reported in the gromacs
guide on line.
i created a file oplsaa.rtp and a file oplsaa.hdb as descrived there, and i
save
On 9/25/14 9:56 AM, Yaser Hosseini wrote:
hi gromacs users
i got this error what can i do??
Program pdb2gmx, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/gmxlib/futil.c, line: 593
File input/output error:
1AKI.pdb
For more information and tips for troubleshooting, please
On 9/25/14 12:38 PM, Neha Shafique wrote:
Hi everybody,
I am running Gromacs 4.6, and simulating a Martini bilayer. For some of the
analysis, I want to separate the bilayer into leaflets and analyze their
data individually. I was wondering if Gromacs had a script or tool that
would allow me
On 9/25/14 2:44 PM, Yaser Hosseini wrote:
hi gromacs users
i wanted to run this command :
grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
but i dont have this file in my folder path:
ions.mdp
how can i get this file in my path.
It appears you are doing my tutorial, so in
On 9/25/14 3:28 PM, Yaser Hosseini wrote:
i dont undrestand it :
In general, an .mdp file is just a text file. Create them in a text editor.
in tutorial i found this:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/Files/ions.mdp
but i dont know how can
On 9/25/14 2:15 PM, yaser wrote:
i did it but i get this error again.
If the file is, in fact in the working directory and has readable permissions,
it is impossible to trigger this error.
-Justin
Sent from my iPad
On Sep 25, 2014, at 19:29, Justin Lemkul jalem...@vt.edu wrote
On 9/26/14 12:23 PM, Yaser Hosseini wrote:
hi gromacs user
i have problem with grompp command in gromacs i cant find .mdp files
and i cant pass step 4 in this tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/04_ions.html
im new in gromacs please
On 9/26/14 6:42 AM, N. S. wrote:
Dear GMX experts,
How could I extract the only state from MD-simulation .TRR (or traj.xtc)
file that has the lowest RMSD from the reference protein.pdb file?
Please give me a line of code in UBUNTU or the script.
Calculate the RMSD using g_rms, find the
On 9/26/14 5:34 AM, GAYATHRI S wrote:
Hello everyone,
I'm running a simulation with Verlet scheme (for GPU).
I've used cut-off method for van der Waals interactions and PME for
electrostatic interactions. For energy minimization, I used steepest
descent, conjugate gradient and l-bfgs
On 9/26/14 12:50 PM, yaser wrote:
thank you for replay
when i want to download this file and i click on it its nothing happend and
just the text page opend and its nothing to download.
Right-click - Save As...
-Justin
--
==
Justin A.
On 9/27/14 12:10 AM, shivangi nangia wrote:
Dear gmx-users,
I am doing a pull simulation in CG MARTINI and following the tutorial:
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
My systems contains POPC and cardiolipin (grouped as Lipid in index
On 9/27/14 4:27 AM, Kim Q Hwan wrote:
Dear all,
I plan to calculate excess chemical potential of bulk water SPC/E model.
mu_water = mu_lj + mu_coulomb. mu_lj was successfully earned from test particle
insertion method.
Problem arises in calculating mu_coulomb. I want to use g_bar method
On 9/27/14 12:39 PM, shivangi nangia wrote:
Thanks Tsjerk and Justin.
I have a follow up question.
To generate separate restraint .itp file for popc and cardiolipin.
genrestr_mpi -f 1shortmd.gro -o posre_card.itp -n 1indexsys.ndx
genrestr_mpi -f 1shortmd.gro -o posre_popc.itp -n
On 9/27/14 3:05 PM, James Starlight wrote:
Dear Gromac's users!
According to tutorials I've noticed that It's important to use position
restrains on the protein (and lipid in case of membrane) during npt
equilibration phase. But in my mind the presence of the restrains on some
part of the
On 9/27/14 3:24 PM, shivangi nangia wrote:
Thanks for the guidance.
Generated posre.itp for popc and cardiolipin for their respective single
molecules.
grompp did not give error.
However, after the pull simulation now, the Protein did not get pull.
COM of Protein before and after 400th
On 9/28/14 7:36 AM, Anurag Dobhal wrote:
I am simulating an RNA molecule in which first residue has a 5'-PO4 cap,
which is uncommon. I am adding the atoms and bond parameters in the .rtp
files in the existing force field directories but these parameters are not
getting saved. I am using Amber
On 9/28/14 7:41 AM, James Starlight wrote:
Thank you very much for the suggestion!
How do you think are there any drammatic differences between different
preassure coupling (barostats) methods implemented not only in Gromacs but
in other md packages like amber and namd? What barostat will be
On 9/28/14 9:14 AM, Anurag Dobhal wrote:
Hey gromacs users
I got the confout.gro file by running the command
mdrun -v -deffnm em -o confout.gro
and then i ran the command perl inflategro.pl confout.gro 0.95 DPPC
0 system_shrink1.gro 5 area_shrink1.dat
but now the teminal says that
On 9/29/14 4:44 AM, Anurag Dobhal wrote:
hello justin
Can you please tell me how will i solvate my system.
which command will i use and what will be my input and output file.
Consult a basic tutorial for this information. The membrane protein tutorial
assumes the user is already familiar
On 9/29/14 5:58 AM, Ebert Maximilian wrote:
Dear list,
I am a little bit confused regarding the preparation needed to use the AMBER FF
in GROMACS 5.0.1. I have a simple PDB file of a protein and I use this as
input to pdb2gmx. I selected the AMBER FF during the creation process:
gmx_mpi
On 9/29/14 8:01 AM, Kester Wong wrote:
Dear all,
I have been using the SWM4-NDP water model that works well with CHARMM27 force
field.
Time out. SWM4-NDP is a polarizable water model, and CHARMM27 is an additive
force field. The two are not compatible. If you're using them together,
On 9/29/14 10:09 AM, Sathish Kumar wrote:
Dear gromacs usres,
I have run the umbrella sampling with the help of tutorial of justinIn
my system rna is binding with gold nanoparticle...to find out the binding
energy i run the umbrella sampling using the space 0.2 nm and i got total
59
On 9/30/14 5:51 AM, Anurag Dobhal wrote:
Hello gromacs users.
I am running GROMACS Tutorial of KALP15 in DPPC.
I am in the step define box and solvate.
after the command
perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
i am getting an error as
Use of
something that you click on to magically open. It's
just a listing of coordinates. Visualize it in VMD. Inspect its contents with
a text editor.
-Justin
I again repeated the tutorial and I am getting the same things.
Thank you again for your time.
On Tue, Sep 30, 2014 at 4:16 PM, Justin Lemkul
On 9/30/14 8:32 AM, h.aliza...@znu.ac.ir wrote:
Dear users,
How can we define potassium ion in GROMOS ions.itp file?
Exactly like the other ions. If there are suitable K parameters, define the
[moleculetype] and add the nonbonded parameters for the new atom type in
ffnonbonded.itp.
On 9/30/14 10:30 AM, Anurag Dobhal wrote:
Dear justin
Thank you for your rely and precious time.
I am aware that .gro file is to be visualized in VMD and its content can be
checked in text editor.
all the previous .gro file are visualized and checked in VMD.
I have obetained that (
On 9/30/14 9:58 AM, Mahboobeh Eslami wrote:
dear Justin
thanks for your reply
The plot of the RMSD against time for the trajectory generated with g_rms shows
a maximum RMSD about 0.195 nm.
I set cut-off value to 0.2 nm for g_clusters command.
Is it a appropriate value?
g_rms and g_cluster do
On 9/30/14 3:31 PM, niyaz.sabir wrote:
Dear Gromacs users,
Is there any tutorial to simulate a protein in water solution containing
neutral zwitterionic osmolite such as trimethylglycine? Evaluating effects of
the compound on protein stability/secondary structure flexibility is to be
On 10/2/14 8:45 AM, ashish bihani wrote:
Hello everyone,Has anyone subjected a polypeptide containing a phosphoserine
residue to :~$ pdb pdb2gmx ? The program does not recognize serine as it has a
phosphorus atom attached to it which is not present in the definition. I am
trying to define
On 10/2/14 8:50 AM, Anurag Dobhal wrote:
Thanks Justin
I m running the command
mdrun -s em.tpr and I did get the confout.gro file as output.
after that I am running the command
perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5
area_shrink1.dat
and then again the energy
On 10/2/14 9:21 AM, xy21hb wrote:
Dear all,
I have used parachem to generate the topology file in .str format.
Since I would like to use it in GROMACS software, I wonder how I can convert it
to CHARMM force field format in GROMACS.
Use our converter:
On 10/2/14 12:51 PM, Anurag Dobhal wrote:
how will I get to know that the system have shrunken enough, and which file
I need to solvate.
This is stated in the tutorial.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA
On 10/2/14 1:39 PM, David Ackerman wrote:
Hello,
I am also attempting to run Martini using version 5 and am getting the same
two errors with an mdp file that worked (aside from warnings) on version
4.6.5. Does anyone have a solution to this problem?
It's because the default cutoff scheme
On 10/6/14 10:35 PM, Kester Wong wrote:
Dear Justin and all,
원본 메일 -
*보낸사람* : Justin Lemkul jalem...@vt.edu
*받는사람* : gmx-us...@gromacs.org
*받은날짜* : 2014년 9월 29일(월) 21:32:13
*제목* : Re: [gmx-users] Problem with constraints in NVT calculations.
On 9/29/14
On 10/7/14 4:17 PM, andrew biedermann wrote:
I am working through the second tutorial from Dr. Justin A. Lemkul's
tutorial site and have run into a problem finding the inflategro.pl file
online. When I try the link in the tutorial I get the error:
Firefox can't find the server at
On 10/8/14 2:26 AM, GAYATHRI S wrote:
Thank you for your suggestions.
I followed your instruction and applied potential modifier during energy
minimization. However, the problem still persists.
Please suggest what to do.
OK, so there's simply a problem with input checking in grompp.
On 10/7/14 10:59 PM, Kester Wong wrote:
Hi Justin,
Thank you for the clarification. I should look into using NAMD.
The new polarisable Drude implementation will surely benefit everyone in the MD
community.
I am looking forward to using it, as with others (I think there was a similar
post
On 10/8/14 7:24 AM, Dawid das wrote:
Dear gromacs experts,
Is it allowed to change constraints algorithm (e.g. from LINCS to SHAKE)
during
MD simulation? Let's say that simulation crashes because LINCS constraints
are
not satisfied. Can I go from LINCS to shake in the middle of simulation and
On 10/8/14 8:57 AM, Kester Wong wrote:
Hi Justin,
Meanwhile, is it possible to implement a self-consistent FF from scratch?
One
example I came across is from the work by Ho and Striolo
titled: Polarizability effects in molecular dynamics simulations of the
On 10/9/14 11:27 AM, Erik Marklund wrote:
Hi,
No, start over from 1. Remember that gro-files are fixed format.
Erik
On 9 Oct 2014, at 16:19, Albert mailmd2...@gmail.com wrote:
thx a lot for the reply.
But if I would like to define atom 100'001, should I just specify 100'001
directly
On 10/9/14 11:32 AM, Albert wrote:
thanks a lot for clarification.
I've got one more question, are the cases the same for plumed.dat file for
patched PLUMED MD simulation in Gromacs?
Presumably. PLUMED interfaces with Gromacs, so I'd have to assume that
fundamental utilities like index
On 10/10/14 2:02 AM, rama david wrote:
Dear Friends,
I want to do the simulation of lipid membrane with peptides. Peptide
concist 8 amino acid.I want to keep the two or four peptide just away from
membrane and
want to see how they interact with membrane.
I choose the DPPC
On 10/10/14 7:36 AM, Kester Wong wrote:
Hi Mark,
I think it was due to the charged groups in my temp. coupling setting; I had
the H3O cation(s) and Cl anion(s) grouped separately:
tc-grps = GRA SOL H3O Cl-
; Time constant (ps) and reference temperature (K)
tau-t
On 10/10/14 4:59 AM, Kester Wong wrote:
Hi Justin and all,
Meanwhile, is it possible to implement a self-consistent FF from
scratch? One
example I came across is from the work by Ho and Striolo
titled: Polarizability effects in molecular dynamics
On 10/10/14 7:51 AM, rama david wrote:
Dear Justin,
Thank you a lot for immediate reply.
One more question:
Should I need to equilibriate the membrane after this one ??
Even Tieleman's pre-equilibrated membranes are only from a few ns of simulation
time; I would always
On 10/10/14 10:45 AM, Barnett, James W wrote:
Good morning,
I'm looking at doing a free energy change with thermodynamic integration with
GROMACS. Specifically I want to grow a molecule and find out the difference
in the free energy. For example, I would like to see the free energy change
On 10/10/14 6:16 PM, Ioanna Styliari wrote:
Dear gmx users,
I am using Gromacs 4.6.5 to simulate some amphiphilic diblock copolymers (for
which I have created the .rtp files) in acetone and water mixtures. I am
using the GROMOS53a6 force field.
At the beginning I used the Automated Topology
On 10/12/14 2:59 PM, Ioanna Styliari wrote:
Thank you both very much for your very useful comments! Just to clarify, when
you say tweak the parameters, would just an investigation of the change of
the charges be sufficient?
There's no way to know that, but hopefully so. The charges from
On 10/13/14 6:27 PM, unipa wrote:
hi,
i wold know how in this file what does means the element in the III and IV
colums?
ffoplsaa.rtp:
; Polyethylene - this is an internal residue
[ Eth ]
[ atoms ]
C1opls_136-0.1201
H11 opls_140 0.0601
H12 opls_140
On 10/13/14 4:48 AM, liuyong_1...@dicp.ac.cn wrote:
Dear gromacs usres,
I want to run nvt simulation of water-ion cluster (Na+(H2O)250) in gas phase
(vacuum) at higher temperature ( bigger than 200 K).
But the cluster will collapse at high temperature. So the distance restraints
is used to
On 10/13/14 8:17 AM, Nilesh Dhumal wrote:
Hello,
I am getting a following error for pdb2gmx.
Fatal error:
Atom O in residue BTC 1 not found in rtp entry with 156 atoms
while sorting atoms
Could anyone tell whats going wrong?
Atoms named O1 or O2 get translated per
On 10/13/14 1:08 PM, Sathish Kumar wrote:
I am not able to find wheather the windows are overlaped or not. Please
help me in this.
You've got a gap in the sampling exactly where g_wham tells you. The histograms
show this. You either need more windows or a different force constant, or
On 10/13/14 8:50 PM, ookami a wrote:
Dear gmx user:
I got this error:Attempting to read a checkpoint file of version 15 with
code of version 12, when i'm running my simulation for npt process.
Anyone know how could i fix this and why does this happen?
I'm running my simulations at Gromacs
On 10/13/14 10:42 PM, Nilesh Dhumal wrote:
hello,
I running grompp for simulation. I get Segmentation fault error.
grompp -f 600.mdp -c cu.gro -p cu_btc_1.top -o 1.tpr
checking input for internal consistency...
processing topology...
Segmentation fault
Could any one tell what is the
On 10/14/14 12:31 AM, RINU KHATTRI wrote:
hello gromacs user i am working on protein ligand complex with popc membrane
i am running production md in extended time (40 ns) i got some file i
am using -noappend option i got confout.gro file in each extended time
what is the use of this file if i
On 10/14/14 7:40 AM, Kester Wong wrote:
Hi Justin and all,
Meanwhile, is it possible to implement a self-consistent FF
from scratch? One
example I came across is from the work by Ho and Striolo
titled: Polarizability effects
On 10/14/14 11:37 PM, Batdorj Batsaikhan wrote:
Dear gmx-users,
Hello, I am working on free energy calculation of a protein. How long run
should be enough for Free Energy Calculation of a protein?
How is it that you're attempting to calculate this quantity?
-Justin
--
Please remember to use a sensible subject line.
On 10/15/14 6:53 AM, Padmani Sandhu wrote:
Hello
I have energy minimized the complex successfully and I dont understand
whats wrong with the system.
What were Epot and Fmax from minimization? Please copy and paste the actual
output. What
On 10/15/14 6:25 AM, RINU KHATTRI wrote:
hello justin
i have been visualized the file of confout.gro file in vmd and the
position of protein and ligand is ok i know i have to analyze all the
parameters like energy and rmsd is it sufficient to extend my
simulation or which file i have to
On 10/15/14 5:06 AM, venkatesh s wrote:
hello
In my task some water molecules in one protein active site and it playing
one of the role of interactions and binding affinity
if i want retain that water molecules in active site to preform the
simulations what i want to do ? further
Simply
On 10/15/14 7:30 AM, Mario Fernández Pendás wrote:
Dear all,
I am still interested in some integrator related issues.
I understand that the easiest way to implement velocity Verlet was to split
the updates in two updates. But I don't understad the order of those
updates.
I mean why there are
On 10/15/14 2:05 PM, Johnny Lu wrote:
Pure md doesn't deal with complex orbitals well, I guess. Hydrogen bonds in
pure md is not directional, as it should be.
can molecular dynamics (md) simulate heavy metals, like iron, which have d
oribtals?
I heard that even calcium is a bit troublesome
.
My question is concerning the situation where you still don't know which
are the salt bridges in the system and, after that, which are the ones
you should take a closer look (I think the obvious approach would be to
search literature, but that is not always successful).
Justin Lemkul has mentioned
On 10/16/14 5:02 AM, elham tazikeh wrote:
Dear users
For calculating free energy of methan (in justin tutorial)
I changed important parameters instead of the parameters in lambda=0 that
having in that tutorial
Is it correct?
If you're trying to execute the tutorial, no, don't make any
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