Hi All,
Any suggestions?
Thanks,
On Mon, Nov 11, 2013 at 12:38 AM, rajat desikan wrote:
> 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 f
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 laye
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 confout
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
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
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 st
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
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,
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 wrote:
>
>
> On 11/12/13 12:30 PM, Venkat Reddy wrote:
>
>> Dear Sir, Thanks for the quick reply.
>> So, I have to declare
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
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 d
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
--
Vi
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 d
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, whi
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.gr
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
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 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
Then, how to mention the direction for spherical particles Sir?
On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul 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*
>>
>> Here I
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
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. Whethe
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:
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Sent from the
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
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
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,
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
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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
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 wrote:
> MSD is 3D by default.
>
>
>
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 g_ana
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 wrote:
>
>
> On 11/11/13 6:56 PM, bh
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 ?
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 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 :-
https://www.
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 wrote:
>
>
> 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,
MSD is 3D by default.
Dr. Vitaly V. Chaban
On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy 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 other tool like g_v
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
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 100
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
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
--
gmx-users mailing list
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:
http://gromacs.5086.x6.na
> Date: Mon, 11 Nov 2013 08:27:05 -0800 (PST)
> From: kolnkempff
> 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 trying to in
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 gu
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 :-
https://www.dropbox.com/s/sovzk40cudznfjw/hbond_115-water
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