Hi,
Today we are migrating the mailinglist server to a new machine, so there
might be delays in the delivery of messages.
Cheers,
Rossen
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Hi Rajat,
If you remove comm on the bilayer, there may be relative comm between
leaflets. If that relative motion is significant and you switch to removing
comm per leaflet, the program suddenly finds itself resetting the com over
a large distance. About equilibration, you equilibrated with
Hi,
Something went wrong earlier in your workflow. Check your log files, etc.
Mark
On Nov 13, 2013 3:57 AM, guozhicheng222 guozhicheng...@126.com wrote:
Hi:
When I am running the ibi procedure, I get the following error message:
A coordinate in file
Hi Tsjerk,
That was very sage advice! Thank you. I will try regenerating velocities
and see if the motion goes away...
On Wed, Nov 13, 2013 at 2:00 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Rajat,
If you remove comm on the bilayer, there may be relative comm between
leaflets. If that
An update to anyone interested:
Regenerating velocities by itself did not solve the problem. I had to
regenerate velocities and couple the upper and lower leaflets separately to
the thermostat to equilibrate the system. To smoothen the equilibration
process further, I used a 0.5 fs timestep
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 of topol.top file. I modified [ molecules ]
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 sorting atoms.
I checked
Dear Justin
My cnt is infinite.
I obtained cnt.top by g_x2top and then modified cnt.top to cnt.itp.
For obtaining cnt.top, I used following files:
---
ffcnt.atp:
CA 12.01100 ; aromatic C
Hello Mark,
I don't get any informing of your reply by e-mail, but get your reply
searched by google.
Anyway thanks very much for your reply!
Yeah, I used two totally different mdp files for the single point
calculation because I thought
that gromcs would report the potential energy of my
Dear All,
can anyone tell me how to construct mixed lipid bilayer in gromacs
id possible also provide me the command to construct the mixed bilayer
Thanks in advance
Nikhil
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Hello, all
I intend to make some modification on minimize.c in mdlib.
Do I need to do cmake make make install all over again?
Or is there a quick way for recompiling?
Thanks for any tips.
JhengWei Li
Institute of Atomic and Molecular Sciences,
Academia Sinica, Taipei 106, Taiwan
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On 11/13/13 12:20 AM, Venkat Reddy wrote:
Dear Justin and Piggot,
Thanks for the suggestions. Actually, I have constructed a CG lipid vesicle
by placing lipids in random conformation in a simulation box. My lipid
system is heterogeneous, i.e., it has different types of lipids
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 of
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
Start with packmol if you want to start from scratch. Or else get a pretty
equilibrated mixed lipid bilayer if available somewhere on web.
On Nov 13, 2013 6:45 PM, Nikhil Agrawal nikhil.08...@gmail.com wrote:
Dear All,
can anyone tell me how to construct mixed lipid bilayer in gromacs
id
Hi Nikhil,
The first step would be to determine what forcefield you are going to use
for the lipids. If you are going to use Charmm or Slipids, you can use
charmmgui (just google it). If you are planning to use the Gromos
forcefields, you can check Prof. Tieleman's website or lipidbook for pure
Let me correct myself :). Its pre-equilibrated. Not pretty equilibrated. :)
On Nov 13, 2013 7:23 PM, Arun kumar V arun.tar...@gmail.com wrote:
Start with packmol if you want to start from scratch. Or else get a pretty
equilibrated mixed lipid bilayer if available somewhere on web.
On Nov 13,
For just modifying a file, just doing make is sufficient. I would
recommend not installing the modified version (since you can run the
build/src/kernel/mdrun directly), or if you must install, to use the
suffixing options available in the ccmake advanced mode.
Mark
On Nov 13, 2013 2:48 PM, Jheng
Probably the default behaviour of pdb2gmx for termini is not appropriate
for your input. Use pdb2gmx -ter and choose wisely
Mark
On Nov 13, 2013 12:03 PM, hasthi durgs7kr...@gmail.com wrote:
Hello GROMACS users,
I have phosphorylated Serine residue in my
protein
Dear Justin,
I have referred to an article (Vuorela T, Catte A, Niemela PS, Hall A,
Hyvonen MT, et al. (2010) Role of Lipids in Spheroidal High Density
Lipoproteins. PLoS Comput Biol 6(10): e1000964.
doi:10.1371/journal.pcbi.1000964), where the authors have clearly described
the fitting of 2D
On 11/13/13 9:41 AM, Venkat Reddy wrote:
Dear Justin,
I have referred to an article (Vuorela T, Catte A, Niemela PS, Hall A,
Hyvonen MT, et al. (2010) Role of Lipids in Spheroidal High Density
Lipoproteins. PLoS Comput Biol 6(10): e1000964.
doi:10.1371/journal.pcbi.1000964), where the authors
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 true?
In my case, peptid + cnt + water
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
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?
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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
Hi GROMACS users,
GROMACS 4.6.4 is officially released. It contains numerous bug fixes, and
some noteworthy simulation performance enhancements (particularly with
GPUs!). We encourage all users to upgrade their installations from earlier
4.6-era releases.
You can find the code, manual, release
Will a simulation from 4.6.1 continue running fine if I upgrade to 4.6.4?
Hi GROMACS users,
GROMACS 4.6.4 is officially released. It contains numerous bug fixes, and
some noteworthy simulation performance enhancements (particularly with
GPUs!). We encourage all users to upgrade their
Hello,
I am trying to run MPI, OpenMP and CUDA enable GROMACS 4.6.3 on nodes having 12
cores (2 CPUs) and 2 GPUs (Tesla M2090) each. The problem is when I launch job
GROMCAS is using only GPUs on first node come across and failing to use GPUs on
other nodes.
The command I used for two gpu
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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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 users,
g_energy -f *.edr -vis
I have two questions about the results of eviscoi.xvg ( derivative of
Einstein relation):
1.) I dont understand the unit of y-axis. It is kg.m^(-1).s^(-1).10^(-3) in
B.Hess 2002
In eviscoi.xvg
@yaxis label (kg m\S-1\N s\S-1\N ps)
That is
The unit of
Sorry, I attached the wrong file . Here's the average file generate from
one of the files I sent in my last mail. I used the command g_analyze -f
hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained
from this command :-
Hi,
I tried g_select to dump the structure with the interacting water
molecules, but I don't know know how to do that. I searched for some
threads in the discussion but wasn't able to find anything related to my
need. Can you explain how can I do that ?
On Tue, Nov 12, 2013 at 7:39 AM, bharat
Date: Mon, 11 Nov 2013 08:27:05 -0800 (PST)
From: kolnkempff kolnkem...@gmail.com
Subject: [gmx-users] installation error under openSuse 12.2
To: gmx-users@gromacs.org
Message-ID: 1384187225465-5012430.p...@n6.nabble.com
Content-Type: text/plain; charset=us-ascii
Dear gmx-users,
I am
Thank you so much Justin. On the one hand, I feel dumb because I could have
sworn that I was using a clean build directory. On the other hand, I
obviously lost track of what I was doing because your suggestion worked like
a charm!
Koln
--
View this message in context:
Dear all,
I am simulating a spherical lipid vesicle. I want to calculate the
diffusion coefficient for each lipid component in 3D. How to calculate it
using g_msd (or any other tool like g_velacc)?
Thank you for your concern
--
With Best Wishes
Venkat Reddy Chirasani
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gmx-users mailing list
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
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 the simulation
from check point file on
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
MSD is 3D by default.
Dr. Vitaly V. Chaban
On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy venkat...@gmail.com wrote:
Dear all,
I am simulating a spherical lipid vesicle. I want to calculate the
diffusion coefficient for each lipid component in 3D. How to calculate it
using g_msd (or any
There are no problems to have ions while using Reaction-Field treatment.
Dr. Vitaly V. Chaban
On Mon, Nov 11, 2013 at 7:06 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/11/13 12:08 PM, Williams Ernesto Miranda Delgado wrote:
Hello
If I did the MD simulation using PME and neutralized
On 11/11/13 5:39 PM, bharat gupta wrote:
Sorry, I attached the wrong file . Here's the average file generate from
one of the files I sent in my last mail. I used the command g_analyze -f
hbond_115-water.xvg -av hbond_115-water-avg.xvg. Here's the file obtained
from this command :-
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
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 know how to do that. I searched for some
threads in the discussion but wasn't able to find anything related to my
need. Can you explain how can I do that
Thanks justin for your replies. I understood the g_analyze related data. I
tired g_analyze to dump the structures as you said. But, I didn't find any
switch that can be used to dump the structure in pdb format.
On Tue, Nov 12, 2013 at 10:15 PM, Justin Lemkul jalem...@vt.edu wrote:
On
On 11/12/13 8:33 AM, bharat gupta wrote:
Thanks justin for your replies. I understood the g_analyze related data. I
tired g_analyze to dump the structures as you said. But, I didn't find any
switch that can be used to dump the structure in pdb format.
Because that's not the function of
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?
On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:
MSD is 3D
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
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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 protein then
I converted it into pr.itp by deleting
As Mark said, please share the *entire* log file. Among other
important things, the result of PP-PME tuning is not included above.
However, I suspect that in this case scaling is strongly affected or
by the small size of the system you are simulating.
--
Szilárd
On Sun, Nov 10, 2013 at 5:28 AM,
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
I run
grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
and everything looks fine. I check the nvt.tpr, and temperature is ok.
the real problem is with the mdrun function.
could be a problem of the software?
Thanks
Javier
Justin Lemkul wrote
On 11/11/13 11:24 AM, Carlos
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?
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Restarting-a-simulation-after-replacing-an-empty-md-trr-file-tp5012443p5012459.html
Sent from
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 check the nvt.tpr, and temperature is ok.
The fact that grompp completes indicates there is nothing syntactically wrong
with the input files.
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
Then, how to mention the direction for spherical particles Sir?
On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul jalem...@vt.edu wrote:
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*
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 jalem...@vt.edu wrote:
On 11/12/13 8:55 AM, Venkat Reddy
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 mismatch,
current program: -1
checkpoint
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
The output of energy minimization was
Potential Energy = -1.42173622068236e+06
Maximum force = 9.00312066109319e+02 on atom 148
Norm of force = 2.06087515037187e+01
Thanks
Javier
Justin Lemkul wrote
On 11/12/13 10:58 AM, cjalmeciga wrote:
I run
grompp -f nvt.mdp -c em.gro -p
On 11/12/13 12:14 PM, cjalmeciga wrote:
The output of energy minimization was
Potential Energy = -1.42173622068236e+06
Maximum force = 9.00312066109319e+02 on atom 148
Norm of force = 2.06087515037187e+01
OK, reasonable enough. How about a description of what the system is,
Dear Sir, Thanks for the quick reply.
So, I have to declare -type no flag. Isn't it??
and I have recently gone through Justin's membrane protein tutorial, where
he has calculated diffusion coefficient for lipids in a membrane by
creating an index group for a particular atom. So, here also shall I
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.
Anyone could help me out.
Thanks
--
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 each spatial dimension. That is precisely what this
option will
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.
Thanks Justin. So, I have to calculate diffusion coefficient three times
(x,y,z) and finally add-up together to get in 3D???
On Tue, Nov 12, 2013 at 11:25 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/12/13 12:30 PM, Venkat Reddy wrote:
Dear Sir, Thanks for the quick reply.
So, I have to
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 together to get in 3D???
If you just want the overall diffusion constant, that's what g_msd does without
any additional options.
-Justin
On Tue,
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 parameters
integrator = md
Hi Venkat,
Can you make it a bit clearer what you actually want?
If it is the diffusion of the lipids along the curved surface of the
vesicle, rather than simply the overall 3D diffusion, this is not
trivial to calculate as I don't believe g_msd will do this for you. This
property has been
Hi Mark and Szilard
Thanks for your both suggestions. They are very helpful.
Neither run had a PP-PME work distribution suitable for the hardware it
was
running on (and fixing that for each run requires opposite changes).
Adding
a GPU and hoping to see scaling requires that there be
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
Hi:
When I am running the ibi procedure, I get the following error message:
A coordinate in file conf.gro does not
contain a '.'
Additionally, I check the coordinate file of confout.gro in step_001. It showed
that 'nan' symbol appeared in
Dear Justin and Piggot,
Thanks for the suggestions. Actually, I have constructed a CG lipid vesicle
by placing lipids in random conformation in a simulation box. My lipid
system is heterogeneous, i.e., it has different types of lipids
(POPC,CHOLESTEROL,PPC...etc). Some of them occupy the outer
Hi All,
Any suggestions?
Thanks,
On Mon, Nov 11, 2013 at 12:38 AM, rajat desikan rajatdesi...@gmail.comwrote:
Hi All,
I am experiencing a few problems in membrane simulations wrt COM removal.
I downloaded a 400 ns pre-equilibrated Slipid-DMPC membrane with all the
accompanying files. I
In addition to my previous question, I have another question about
g_analyze. When I used the hbond.xvg file to get the average and plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its final calculation gives 7.150
as the average
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 31 steps using 20001 frames', appeared
On 11/11/13 1:30 AM, bharat gupta wrote:
thank you informing about g_rdf...
Is it possible to dump 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 ??
g_select
On 11/11/13 4:06 AM, bharat gupta wrote:
In addition to my previous question, I have another question about
g_analyze. When I used the hbond.xvg file to get the average and plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its
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
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
directly to their website. Now I am at the make
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
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 index.ndx -o nvt.tpr
mdrun -deffnm nvt
Nevertheless, I got
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
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.
Thanks
Williams
--
gmx-users mailing listgmx-users@gromacs.org
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 water-water hydrogen bonds around two Na+ ions,it
On Nov 10, 2013 10:04 AM, Mark Abraham mark.j.abra...@gmail.com wrote:
Yes (unless you are using AMD cpus), per the installation instructions,
although you will probably do slightly better with GCC 4.7, and should not
do a new install of 4.6.2 after 4.6.3 is released. In particular, 4.6.2 has
On Sun, Nov 10, 2013 at 5:28 AM, Dwey Kauffman mpi...@gmail.com wrote:
Hi Szilard,
Thank you very much for your suggestions.
Actually, I was jumping to conclusions too early, as you mentioned AMD
cluster, I assumed you must have 12-16-core Opteron CPUs. If you
have an 8-core (desktop?)
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 pull_geometry = distance, so, I should fix
Thank you Justin for your kind help. The simple reason for considering only
gromos parameter sets is that the parameters for the metal ions (in my
protein) are not defined in other force fields.
On Sat, Nov 9, 2013 at 7:18 PM, Justin Lemkul [via GROMACS]
ml-node+s5086n5012376...@n6.nabble.com
Dear all
I encounter a problem while running command mdrun_mpi -v -deffnm em in
gromacs.
I am new to the gromacs. i just ran test calculation, *simulation of
lyzozyme in water*. i am able to generate gro, tpr files. But in the final
step i got following error.
Thanks in advance.
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 11/10/13 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
Hi,
There's nothing GROMACS-specific here - something about your MPI
installation, configuration or use is pretty wrong, but we can't help work
out what.
Mark
On Sun, Nov 10, 2013 at 12:31 PM, S.Chandra Shekar
chandrashe...@iisertvm.ac.in wrote:
Dear all
I encounter a problem while
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
much more massive than the pulling group.
I want
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
much
Hi All,
I am experiencing a few problems in membrane simulations wrt COM removal. I
downloaded a 400 ns pre-equilibrated Slipid-DMPC membrane with all the
accompanying files. I then carried out the following steps:
1) energy minimization
2) NVT Eq - 100 ps
3) NPT Eq - 250 ps (Berendsen temp, Pres
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 average of actual hbonds (2nd column ) and SS2 is the average of 3rd
column. Am I right here or not ??
I tried to calculate the h-bond for residues
Justin, thank you very much for your kind help about LIE and PME
Williams
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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
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