On 11/13/13 11:53 AM, Atila Petrosian wrote:
Dear Justin
Thanks for your quick reply.
I was confused.
If I add #include "ffcntbon.itp" after #include "cnt.itp" in .top file,
my problem was solved and error was solved?
No. The parameters are at the force field level and thus have to be #i
On 11/13/13 10:39 AM, Atila Petrosian wrote:
Dear Justin
Thanks for your reply.
In your previous setup, you were effectively trying to use CHARMM27 + some other
force field related to the CNT. You can't do that.
Thus, Gromacs is not appropriate for systems containing cnt.
Is my deduction
n the
configuration and calculates relative to it. I suspect you will need to modify
the code to implement a custom algorithm.
-Justin
) and 3D diffusion coefficient to the core lipids.
On Wed, Nov 13, 2013 at 7:19 PM, Justin Lemkul wrote:
On 11/13/13 12:20 AM, Venkat Reddy wrote:
Dear Justi
On 11/13/13 6:02 AM, hasthi wrote:
Hello GROMACS users,
I have phosphorylated Serine residue in my
protein (140 residues) of interest, now when I run pdb2gmx I get this
following error
Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms
while
On 11/13/13 5:51 AM, Atila Petrosian wrote:
Dear Justin
Very thanks for your reply.
I created a new topol.top file as below:
1) I used once default directive.
2) I put cnt.itp file in working directory.
3) I copied pr.top and renamed it to topol.top. I added #include "cnt.itp"
in the end o
literature for
papers simulating vesicles to see how the lipid diffusion was calculated.
Cheers
Tom
On 11/12/2013 06:35 PM, Justin Lemkul wrote:
On 11/12/13 1:33 PM, Venkat Reddy wrote:
Thanks Justin. So, I have to calculate diffusion coefficient three times
(x,y,z) and finally add-up togeth
On 11/12/13 1:47 PM, Rama wrote:
Hi Justin,
Below I pasted .mdp file and topology. In .log file I could see energy term
for position restraints.
.mdp file---
title = NPT Equilibration
define = -DPOSRES ; position restraints for protein
; Run paramet
n Tue, Nov 12, 2013 at 11:25 PM, Justin Lemkul wrote:
On 11/12/13 12:30 PM, Venkat Reddy wrote:
Dear Sir, Thanks for the quick reply.
So, I have to declare -type no flag. Isn't it??
The options for the -type flag are x, y, or z. You said you wanted the
diffusion coefficient in ea
On 11/12/13 12:35 PM, Rama wrote:
Hi Gromacs users,
I'm doing protein-Bilayer MD simulations. Enzyme contains structural zinc
and calcium ions during Energy minimization, NVT and NPT stage, ions are
changing there position even though I applied position restraints for the
atoms and ions.
Any
se-grained system.
Yes, a representative atom is usually what is passed to g_msd.
-Justin
On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul wrote:
On 11/12/13 11:25 AM, Venkat Reddy wrote:
Then, how to mention the direction for spherical particles Sir?
Read g_msd -h again, payin
, which
force field you chose, how you derived the ligand topology, and the full
contents of your .mdp file?
-Justin
Thanks
Javier
Justin Lemkul wrote
On 11/12/13 10:58 AM, cjalmeciga wrote:
I run
grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
and everything looks fine. I
On 11/12/13 12:07 PM, arunjones wrote:
Thank you Sir,
initially i was running on 60 threads, now i changed it to 100. simulation
is running with out any error, but i found a note in the log file as fallows
#nodes mismatch,
current program: 100
checkpoint file: 60
#PME-nodes mi
On 11/12/13 11:25 AM, Venkat Reddy wrote:
Then, how to mention the direction for spherical particles Sir?
Read g_msd -h again, paying specific attention to the -type flag.
-Justin
On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul wrote:
On 11/12/13 8:55 AM, Venkat Reddy wrote:
Thank
On 11/12/13 11:10 AM, arunjones wrote:
Hello Sir,
Thanks for the reply.
now is it fine if i use 100 threads in my restart.
is there any impact on the over all simulation?
Only if that is the number of threads originally used in the run. If not, there
will be a mismatch between the DD grid
).
the real problem is with the mdrun function.
could be a problem of the software?
You have presented no evidence that would lead anyone to believe the problem is
with mdrun. In the vast majority of cases, user input is the problem.
-Justin
Thanks
Javier
Justin Lemkul wrote
On 11/11
On 11/12/13 10:07 AM, Atila Petrosian wrote:
Dear all
My system contains protein + cnt + water molecules.
I have summarized what I did below:
---
1) By pdb2gmx and charmm27 force field, I obtained pr.top for prot
On 11/12/13 8:55 AM, Venkat Reddy wrote:
Thank you sir for the prompt reply.
*g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o msd.xvg -tu ns*
Here I am giving -lateral z (like for membrane simulations). Is it fine for
spherical systems also?
No. The system is a sphere, so what use
unction of g_analyze. Use trjconv -dump with a suitable
index file (from g_select).
-Justin
On Tue, Nov 12, 2013 at 10:15 PM, Justin Lemkul wrote:
On 11/11/13 6:56 PM, bharat gupta wrote:
Hi,
I tried g_select to dump the structure with the interacting water
molecules, but I don't know
mplies that on average 7 hydrogen
bonds are formed during the simulation time of 5ns to 10ns. What does then
the average file or its graph tells ??
On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul wrote:
On 11/11/13 4:06 AM, bharat gupta wrote:
In addition to my previous question, I have
On 11/12/13 1:15 AM, arun kumar wrote:
Dear Gromacs users,
I am running a 50ns simulation of a protein having nearly 700 residues on
60 threads (Gromacs 4.6.3).
At one point i got a disk space problem, so i have deleted the md.trr file
and created an empty md.trr file. when i tried to restart
as is intuitive from your values. An
average of 4 is impossible if all the data points are in the range of 6-9.
-Justin
On Mon, Nov 11, 2013 at 9:58 PM, Justin Lemkul wrote:
On 11/11/13 4:06 AM, bharat gupta wrote:
In addition to my previous question, I have another question about
g
On 11/11/13 12:08 PM, Williams Ernesto Miranda Delgado wrote:
Hello
If I did the MD simulation using PME and neutralized with ions, and I want
to rerun this time with reaction field zero, is there any problem if I
keep the ions? This is for LIE calculation. I am using AMBER99SB.
Why do you th
On 11/11/13 12:36 PM, Sushma Yadav wrote:
Dear gromacs users,
I have NaCl-water system of finite concentration .I want to calculate
water-water hydrogen bond in the first solvation shell around ion..So I
used g_hbond -shell option.For single ion in water,its easy to
calculate..But say,for wate
On 11/11/13 11:27 AM, kolnkempff wrote:
Dear gmx-users,
I am trying to install gromacs-4.6.3 on an older Dell that is running
openSuse 12.2
Using "DGMX_BUILD_OWN_FFTW=ON" failed for me so to get through cmake I had
to compile fftw from scratch and I followed the recommendation of going
direct
On 11/11/13 11:24 AM, Carlos Javier Almeciga Diaz wrote:
Hello evryone,
I doing a simulation of a ligand-protein interaction with gromacs 4.5.5.
Everything looks fine after I equilibrate the protein-ligand complex. I'm
running these commands:
grompp -f nvt.mdp -c em.gro -p topol.top -n ind
On 11/11/13 5:04 AM, guozhicheng222 wrote:
Hi
I am confusing with the output file (.log) about the sample frequency
(frames) in my simulation. The average information in .log file is
'Statistics over 31 steps using 3001 frames' where nstxout =4000 and
nstlog =4000. While, 'Statistics over
p the structure with those average water molecules
interacting with the residues. I generated the hbond.log file which gives
the details but I need to generate a figure for this ??
On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul wrote:
On 11/10/13 8:38 PM, bharat gupta wrote:
But trjorder
-Justin
On Mon, Nov 11, 2013 at 10:40 AM, Justin Lemkul wrote:
On 11/10/13 8:38 PM, bharat gupta wrote:
But trjorder can be used to calculate the hydration layer or shell around
residues ... Right ??
Yes, but I also tend to think that integrating an RDF is also a more
straightforward way
that may or may not be an informed decision - with an RDF it is clear where the
hydration layers are.
-Justin
On Mon, Nov 11, 2013 at 10:35 AM, Justin Lemkul wrote:
On 11/10/13 8:30 PM, bharat gupta wrote:
Thanks for your reply. I was missing the scientific notation part. Now
everything
On 11/10/13 8:30 PM, bharat gupta wrote:
Thanks for your reply. I was missing the scientific notation part. Now
everything is fine.
Regarding trjorder, it doesn't measure h-bonds but gives the water nearest
to protein.
I wouldn't try to draw any sort of comparison between the output of trjo
On 11/10/13 7:18 PM, bharat gupta wrote:
I checked the file hbnum.xvg file and it contains three columns - time,
hbonds, hbonds that donot follow the angle criteria. In that case SS1 is
The third column is not actually H-bonds, then ;)
the average of actual hbonds (2nd column ) and SS2 is t
On 11/10/13 9:14 AM, shahab shariati wrote:
Dear Justin
Very thanks for your reply.
What you described earlier should not be attempted with "distance"
geometry. It won't work very well. The use of restraints is almost
NEVER necessary, especially in the case where the reference group > is
mu
On 11/10/13 5:31 AM, shahab shariati wrote:
Dear Justin
Thanks for your reply.
You are right. I should not extrapolate too literally from your tutorial
to my system.
But, I have a general question:
There is 2 groups in COM pulling method (reference group + pull group).
If I want to use pu
On 11/10/13 12:20 AM, bharat gupta wrote:
Hi,
I used the command g_hbond to find h-bond between residues 115-118 and
water. Then I used g_analyze to find out the average and it gives the value
for the hbonds like this :-
std. dev.relative deviation of
On 11/9/13 9:51 PM, Gianluca Interlandi wrote:
On Sat, 9 Nov 2013, Gianluca Interlandi wrote:
Just to chime in. Here is a that paper might be helpful in understanding the
role of cuoffs in the CHARMM force field:
AU STEINBACH, PJ
BROOKS, BR
AF STEINBACH, PJ
BROOKS, BR
TI NEW SPHERICAL
. If someone else can comment, that
would be useful to me, as well!
Test carefully and please report back. A comparison between CPU and GPU would
be very valuable.
-Justin
On Fri, Nov 8, 2013 at 7:19 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5012351...@n6.nabble.com> wrote:
debugger to see which function is failing.
-Justin
On Sat, Nov 9, 2013 at 7:16 PM, Justin Lemkul wrote:
On 11/9/13 5:24 AM, rajat desikan wrote:
Hi All,
I have a few older membrane simulations for which the COM for the upper
and
lower leaflets were not removed in the course of the
On 11/9/13 9:38 AM, shahab shariati wrote:
Dear Justin
Thanks for your explanation.
My system contains lipid bilayer + drug + water molecules.
I want to calculate Potential of mean force as a function of the distance
between the centers of mass of drug and the lipid bilayer.
Box vector alon
On 11/8/13 3:32 PM, Williams Ernesto Miranda Delgado wrote:
Greetings again
If I use a salt concentration for neutralizing the protein-ligand complex
and run MD using PME, and the ligand is neutral, do I perform ligand MD
simulation without adding any salt concentration? It could be relevant fo
On 11/8/13 2:27 PM, Williams Ernesto Miranda Delgado wrote:
Greetings
The discussion list had helped me about understanding what to do when I
want to calculate binding free energy using LIE after doing MD simulation
using PME.
Now I need your help about choosing the simulation box size for liga
On 11/9/13 8:22 AM, shahab shariati wrote:
Daer Justin
I studied your tutorial (Umbrella Sampling). It is very beneficial for me.
The system you considered was the dissociation of a single peptide from the
growing end of an protofibril.
You considered following parameters:
Chain_B: referenc
On 11/9/13 5:24 AM, rajat desikan wrote:
Hi All,
I have a few older membrane simulations for which the COM for the upper and
lower leaflets were not removed in the course of the simulations. These are
pretty long simulations exceeding 300 ns.
I have trouble with post-processing of the trajector
On Fri, Nov 8, 2013 at 12:10 AM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5012325...@n6.nabble.com> wrote:
On 11/7/13 12:14 PM, pratibha wrote:
My protein contains metal ions which are parameterized only in gromos
force
field. Since I am a newbie to MD simulations, it would be difficu
On 11/8/13 7:44 AM, vidhya sankar wrote:
Dear Justin Thank you for your Previous reply,
I am trying to Install gromacs 4.6.2 in a cluster having centos
OS with teh Following Command I got following error
cmake ..
-DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON
-DGMX_DOUBLE=ON
CMake Warning at
On 11/7/13 11:32 PM, Rajat Desikan wrote:
Dear All,
The setting that I mentioned above are from Klauda et al., for a POPE
membrane system. They can be found in charmm_npt.mdp in lipidbook (link
below)
http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html
Is there any reason not to use their
On 11/7/13 12:14 PM, pratibha wrote:
My protein contains metal ions which are parameterized only in gromos force
field. Since I am a newbie to MD simulations, it would be difficult for me
to parameterize those myself.
Can you please guide me as per my previous mail which out of the two
simulat
On 11/7/13 8:24 AM, Anirban wrote:
Hi ALL,
Is there any way to get the percentage of each secondary structural content
of a protein using do_dssp if I supply a single PDB to it?
The output of scount.xvg has the percentages, but it's also trivial to do it for
one snapshot. The contents of s
On 11/7/13 6:27 AM, Arunima Shilpi wrote:
Dear Sir
Presently I am working with the example file as given in the umbrella
sampling tutorial.
While running the following command
grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr
I got the following error. How to debu
On 11/6/13 4:52 PM, Mark Abraham wrote:
On Wed, Nov 6, 2013 at 8:22 PM, Justin Lemkul wrote:
On 11/6/13 2:14 PM, Ehsan Sadeghi wrote:
Many thanks Justin. What is an appropriate cut-off value? My box size is
d=
0.5 nm; based on the definition of cut-off radius, its value shouble be
be for your chosen force field.
http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention
-Justin
Cheers, Ehsan
- Original Message - From: "Justin Lemkul" To:
"Discussion list for GROMACS users" Sent: Wednesday,
November 6, 2013 11:22:09 AM Sub
settings. You haven't said which one you're using, and there may be
slight differences between them. If the value you're using isn't taken directly
from a paper, it's not credible.
-Justin
Cheers, Ehsan
- Original Message - From: "Justin Lemkul"
On 11/6/13 1:52 PM, Steve Seibold wrote:
Hello
I am having trouble running a dimmer invacuo simulation. I can do energy
minimization on it, but when I attempt to generate md.tpr file I get this
weird message about “Group Protein not found in index”. I don’t see why I
would need an index file.
On 11/6/13 12:53 PM, Ehsan Sadeghi wrote:
Hi gmx users,
I have simulated ionomer in water solution using gromos force field. But in
middle of simulation(after 2 ns) the simulation stopped and I received these
messages:
WARNING: Listed nonbonded interaction between particles 174 and 188
at
On 11/6/13 10:55 AM, rankinb wrote:
Hi all,
I would like to calculate the number of water molecules around any of the
methyl carbon atoms of tert-butyl alcohol. Currently, I have defined an
index group containing all three of the methyl carbon atoms and used
trjorder -nshell to calculate the
On 11/6/13 5:47 AM, Kavyashree M wrote:
Dear users,
Sorry for repeating the same question. I just wanted to know
whether is it ok if I have rlist > rcoulomb in ligand-water and
prot-lig-water rerun md (with RF-0) while having rlist = rcoulomb
in the original simulation using PME?
The energi
On 11/5/13 7:14 PM, Stephanie Teich-McGoldrick wrote:
Message: 5
Date: Mon, 04 Nov 2013 13:32:52 -0500
From: Justin Lemkul
Subject: Re: [gmx-users] Analysis tools and triclinic boxes
To: Discussion list for GROMACS users
Message-ID: <5277e854.9000...@vt.edu>
Content-Type: text/plain; c
On 11/5/13 10:34 AM, J Alizadeh wrote:
Hi,
I need to replace an atom with another in the considered system.
I'd like to know if it is possible and if so what changes I need to do.
The coordinate file replacement is trivial. Just open the file in a text editor
and repname the atom. The top
On 11/5/13 7:37 AM, MUSYOKA THOMMAS wrote:
Dear Users,
I am running MD simulations of a protein-ligand system. Sometimes when i do
an mdrun, be it for the energy minimization or during the nvt and npt
equillibration or the actual md run step, sometimes the output files are
named in a very odd
what I suggested before. The reason for a large force is
either (1) bad atomic clashes that should be apparent upon visual inspection or
(2) bad topology for the drug.
-Justin
On Tue, Nov 5, 2013 at 5:44 PM, Justin Lemkul wrote:
On 11/5/13 6:28 AM, Kalyanashis Jana wrote:
Hi
On 11/5/13 7:19 AM, Kalyanashis wrote:
I have given my .mdp file,
; title = trp_drg
warning = 10
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps
On 11/5/13 3:45 AM, kiana moghaddam wrote:
Dear GMX Users
I am using parmbsc0 force field to study DNA-ligand interaction but my problem
is free energy calculation (MMPBSA) for this interaction. How can I calculate
free energy using MMPBSA approach?
Thank you very much for your time and c
On 11/5/13 6:28 AM, Kalyanashis Jana wrote:
Hi,
Whenever I am trying to do position retrained MD run, It has been stopped
at middle of the MD run. I have given the following error. Can you please
suggest me something to resolve this error?
Energy minimization has stopped, but the forces have
On 11/4/13 5:25 PM, Ehsan Sadeghi wrote:
Hi gmx users,
I want to simulate ionomer is mixed solution of water and ethanol using gromos
force field.
I tired to follow the steps suggested on gromacs website, which are:
1- Determine the number of co-solvent molecules necessary, given the box
On 11/4/13 2:25 PM, Gianluca Interlandi wrote:
Dear Mark,
Sorry for replying to an older thread. We are trying to perform implicit solvent
simulations of protein G with CHARMM27 in gromacs. We are trying to trouble
shoot why the protein unfolds after already 2 ns of dynamics. We use simulated
On 11/4/13 3:03 PM, Steve Seibold wrote:
Hi Justin
Thanks for your response. Here are the files you asked for. They are all text
files. I am still attempting to fix this, but am still getting the error I
described no matter what I have done so far.
The list does not accept attachments, nor
On 11/4/13 1:29 PM, Stephanie Teich-McGoldrick wrote:
Dear all,
I am using gromacs 4.6.3 with a triclinic box. Based on the manual and mail
list, it is my understanding that the default box shape in gromacs in a
triclinic box. Can I assume that all the analysis tools also work for a
triclinic
On 11/4/13 1:29 PM, Steve Seibold wrote:
Hello
I am just trying to do a simple MD on a dimmer system (in which the dimmers are
NOT identical). I can use pdb2gmx to create a topology file and four .itp
files pores.chainA.itp, pores.chainX.itp; system.Protein.chainA.itp and
system.Protein.
On 11/4/13 8:55 AM, kiana moghaddam wrote:
Dear Justin
It is obvious that emtol value can not be zero or negative. but you wrote in
your email " For more sensitive calculations like free energy simulations and
normal modes, you will want to minimize much more thoroughly (for NM, emtol <
1) and
that are
simply read from the last few lines of the .top though, so there's no need to
invoke any other accessory programs.
-Justin
On Mon, Nov 4, 2013 at 12:19 PM, Justin Lemkul wrote:
On 11/4/13 7:14 AM, Ankita Naithani wrote:
Hi Justin,
Thank you for your reply. I did give the
On 11/4/13 7:14 AM, Ankita Naithani wrote:
Hi Justin,
Thank you for your reply. I did give the .tpr file but the job terminated
after few frames only. Also, if that is not helpful, do you have any
There are no frames in a .tpr file. I suspect you're simply issuing the command
incorrectly,
On 11/4/13 5:06 AM, Ankita Naithani wrote:
Hi,
I was wondering if anyone could help me with the gmxcheck function? In the
manual it is written, -m flag is given a LaTeX file will be written
consisting of a rough outline for a methods section for a paper.
I tried it several times but there isn'
On 11/4/13 3:29 AM, kiana moghaddam wrote:
Dear Justin
Further to your previous email, I want to calculate free energy for DNA-ligand
interaction. According to your answer, for more sensitive calculations like
free energy simulations and normal modes, emtol should be lower than 1. As I
unde
On 11/4/13 3:16 AM, Ramon Valencia wrote:
Hello Dear GROMACS users,
I trying to do a MD calculation using GROMACS, but when I running pdb2gmx I
get the following error:
Fatal error:
Residue '' not found in residue topology database
I'm a beginner GROMACS user, but I want to know exactly, ho
On 11/4/13 1:52 AM, Saman Shahriyari wrote:
dear gmx users
i am trying to use g_lie tool regarding the fact i am a
newbie to this. so i searched through the web for an appropriate
protocol. although there are lots of staffs discussing the theory, but i
couldn't find any thing describing the
On 11/4/13 1:31 AM, Gianluca Interlandi wrote:
Is there a way to tell from the log file whether positional restraints are
really activated or not?
Yes, there is a position restraint energy term written to the .log and .edr
files if the restraints are active.
-Justin
--
==
On 11/3/13 7:12 AM, rankinb wrote:
That last procedure works. I really appreciate your help. The only other
question I have is related to the selection process. Is there a way to
select the oxygen atoms of water within a certain distance of a molecule, as
well as the corresponding hydrogen a
On 11/3/13 12:38 AM, Gianluca Interlandi wrote:
Is it possible to use position restraints:
define = -DPOSRES
during an energy minimization? I tried to do that but it looks like all atoms
are moved during minimization:
Depending on the forces present in the system, it is possible that the a
On 11/3/13 6:20 AM, kiana moghaddam wrote:
Dear Justin
Further to your previous email, I want to calculate free energy for DNA-ligand
interaction. According to your answer, for more sensitive calculations like free
energy simulations and normal modes, emtolshould be lower than 1. As
I understa
0.000
240.0000.0000.0000.0000.000
260.0000.0000.0000.0000.000
…
Thanks in advance,
Xu Huang
On Nov 2, 2013, at 6:35 PM, Justin Lemkul wrote:
On 11/2/13 6:29 PM, Xu Dong Huang wrote:
Dear All,
My martini system has 3
On 11/2/13 6:50 PM, Xu Dong Huang wrote:
@ Gromacs users,
so I did g_dist , and I’m confused by a couple of things. 1) why is it asking
me for 2 groups? I have my particles of interest under 1 type, namely [ O1 ] 1
23, and nothing else. 2) I just picked the same group twice, and the
On 11/2/13 6:29 PM, Xu Dong Huang wrote:
Dear All,
My martini system has 3 particles in a chain, rest is martini water, and I’m only
interested in the bond length distribution of particle 1&2, 1&3 and 2&3, and I
execute the following:
g_bond -f npt.xtc -n index.ndx -o bonds.xvg
I get the fo
On 11/2/13 3:38 PM, kiana moghaddam wrote:
Hi GMX Users
I 'm running MD Simulation for DNA-ligand interaction. I ran energy
minimization with emtol=10, 100 and 250 in 1 steps (steepest descent
followed by the conjugate gradient algorithm). The lowest value for energy
obtained for emtol=
On 11/2/13 12:25 PM, rankinb wrote:
Here are the steps that I used:
1. trjconv -pbc whole -dump 37.875
2. trjconv -pbc nojump
3. trjconv -center
4. g_select to make an index containing the atoms of interest
5. trjconv to extract coordinates
Regardless of whether step 1 is used or not, th
On 11/2/13 12:14 PM, Kavyashree M wrote:
Sir,
Thank you. Should the ligand-water MD be done without PME?
I already answered this. Please read my previous reply again.
-Justin
Thank you
Regards
Kavya
On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul wrote:
On 11/2/13 1:22 AM
On 11/2/13 11:23 AM, rankinb wrote:
Tsjerk,
Thanks for your reply. I have tried using the center option, but ran into
similar problems. Here are the exact commands that I used:
g_select -f file.xtc -s file.tpr -n index.ndx -select 'group 14 and within
0.71 of group 13' -b 37.875 -e 37.875 -
On 11/2/13 1:22 AM, Kavyashree M wrote:
Dear Users,
Its mentioned in the list that it would be
wrong to use g_lie on a simulation which
uses PME.
So kindly suggest any other way available
to get the free energy of ligand binding other
using g_lie?
The original simulation should be done wit
On 11/2/13 6:32 AM, Hossein Lanjanian wrote:
Thank Justin for your help
What forcefield is most suitable to study this case?
The one that your careful study of the literature tells you is the most
reliable. It's up to you to justify your choice, not what someone on the
Internet tells you :
On 11/2/13 1:00 AM, Kavyashree M wrote:
Dear Gromacs users,
I have a protein-ligand in water simulation (Gmx 4.5.3), for
calculating free energy of ligand binding, a separate simulation
of ligand in water simulation is required (which I read from the
list). The question is the protein-ligand i
On 11/1/13 8:39 AM, xiao wrote:
It is impossible. But you can add proton to the acidic amino acid.
It's certainly not impossible. There are constant-pH methods that exist; the
list archive contains many posts on this topic, and more information can be
found at:
http://www.gromacs.org/Do
On 11/1/13 5:37 AM, xiao wrote:
Dear all gromacs users,
I have run a protein-ligand simulations. However, the position of the ligand
is not reasonable after 10ns simulation. There is no problem with the force
field paramers of the ligand. I am trying to constrict the ligand move for
500ps simu
On 10/31/13 7:03 PM, Ehsan Sadeghi wrote:
Thanks Justin,
Here is the steps that I followed:
pdb2gmx -f eth.pdb -o eth.gro -p eth.top
pdb2gmx -f ionomer-4.pdb -o ionomer4.gro -p ionomer4.top
editconf -f ionomer4.gro -o box.gro -bt dodecahedron -d 0.5
genbox -cp box.gro -cs spc216.gro -c
this approach makes
no sense to me (there is a huge difference between 90 and 130). If the target
is 90, set it for 90. Tune the force constant to match the distribution.
-Justin
Thanks,
On Oct 31, 2013, at 4:48 PM, Justin Lemkul wrote:
On 10/31/13 4:44 PM, Xu Dong Huang wrote:
@ Justi
On 10/31/13 4:44 PM, Xu Dong Huang wrote:
@ Justin,
I did not define [angles] in the topology but I do have the angles result
from All-atom run using OPLS forcefield. The reason for me not to include it
in MARTINI forcefield topology is because I wanted to see if it will produce
similar angle
On 10/31/13 4:22 PM, Xu Dong Huang wrote:
@ Justin,
That doesn’t sound very good. I tried it as he suggested using make_ndx, it
seems to work, but it’s not reporting the result I want. When I use g_angle
using the index i created, I chose the group I want to assess (My compound is
very simple
On 10/31/13 2:21 PM, rajat desikan wrote:
Hi,
In the CHARMM36 paper (Klauda et al., JPCB 2010), only the hydrogen bonds
are constrained for the lipid simulations using SHAKE (excerpt from the
paper below)
"Consistent for all of these simulations was the use of a 1 fs time step
and constraining
On 10/31/13 2:25 PM, Ehsan Sadeghi wrote:
Hi gmx users,
I want to solvate nafion molecules in a 3:1 ethanol water solution. I used
genbox with -ci option to add ethanol to water when generating the box, but
it did not work. Then, first I solvated the ethanol in water, and then added
What "di
On 10/31/13 3:59 PM, Riccardo Concu wrote:
Dear Xu,
you have to use the make_ndx option if I'm not wrong.
The syntax should be make_ndx -f xxx.gro -o index.ndx
make_ndx is not particularly useful for angles. To get it to recapitulate the
function of mk_angndx, it's as much work as writing t
?
What version of Gromacs are you using? With 4.6.3, I get sensible output.
-Justin
Thanks for your input,
Xu Huang
On Oct 31, 2013, at 1:38 PM, Justin Lemkul wrote:
On 10/31/13 1:36 PM, Xu Dong Huang wrote:
Dear all.
Since I am interested in finding the average angle, dihedrals in
On 10/31/13 1:36 PM, Xu Dong Huang wrote:
Dear all.
Since I am interested in finding the average angle, dihedrals in my system, I
attempted to use g_angle, but then I realized I need to make index file using
mk_angndx,
I issued the following:
mk_angndx -s npt.tpr -n angle.ndx
and then i us
On 10/31/13 11:40 AM, Nilesh Dhumal wrote:
Could you tell how can I get rid of following warning?
WARNING 1 [file test.top, line 263]:
The bond in molecule-type BMI between atoms 10 C10 and 23 H23 has an
estimated oscillational period of 1.2e-03 ps, which is less than 5 times
the tim
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