Dear Sir/Madam
I am running simulations on a membrane protein using Desmond and I
want to calculate area per lipid for the entire trajectory. I can
convert the trajectories to those of Gromacs using VMD. What else do I
need in order to calculate area per lipid using Gromacs?
Thanking you
Regards
Hi Gromacs users,
I seem to face some problems with my REMD dynamics.
I follow as much as possible the set up description of:
http://jcp.aip.org/resource/1/jcpsa6/v135/i14/p145102_s1?isAuthorized=no
Just to summarise:
Alanine dipeptide in explicit water: minimization, nvt, and npt equilibration
a
Hi,
Did you call your genrestr output in your mdp file using define = * ? (for
example define = -DPOSRES ; where posres was your file name.)
Thanks
Peterson J
--
View this message in context:
http://gromacs.5086.n6.nabble.com/question-about-minimisation-tp4999681p4999685.html
Sent from the G
Did you try --disable-shared? In recent versions of GROMACS shared
libraries are the default but libmopac.a is static. I would expect a
compilation error regarding this issue; does it come up when doing make?
You can also add --disable-threads as you cannot use parallelization in
GROMACS with
Dear Gromacs users,
I have a query regarding the number of bins used in wham analysis.
If I have performed by simulations over 15 umbrellas (15 different
staring structures), what should be the ideal number of bins to
perform wham analysis? Does it depend on the number of umbrellas. For
example:
Ho,
first I minimize my structure. This is the corresponding mdp file:
define = -DPOSRES
integrator = steep
emtol = 10
nsteps = 1500
nstenergy = 1
energygrps = System
coulombtype = PME
rcoulomb=
On 26/07/2012 5:32 PM, Antonia Mey wrote:
Hi Gromacs users,
I seem to face some problems with my REMD dynamics.
I follow as much as possible the set up description of:
http://jcp.aip.org/resource/1/jcpsa6/v135/i14/p145102_s1?isAuthorized=no
Just to summarise:
Alanine dipeptide in explicit water:
On 26/07/2012 3:27 PM, Priyanka Shah wrote:
Dear all,
I want to apply distance restraint between Zn and its coordinating
atoms. Zn is supposed to be in octahedral geometry. Zn is making
coordination bond with O of hydroxyl group in ligand atom also. Even
after several attempts, it seems like des
On 26/07/2012 4:47 PM, radhika jaswal wrote:
Hi all,
I ran a simulation of a molecule in box. The molecule was intact during the
position restraint step, bit after the final md of 1 ns it broke down into 2
parts. I am using the GroMACS version 4.5.4 and Berendsen thermostat with ref_t
= 300 K
On 26/07/2012 5:01 PM, Nidhi Jatana wrote:
Dear Sir/Madam
I am running simulations on a membrane protein using Desmond and I
want to calculate area per lipid for the entire trajectory. I can
convert the trajectories to those of Gromacs using VMD. What else do I
need in order to calculate area per
On 26/07/2012 6:47 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Ho,
first I minimize my structure. This is the corresponding mdp file:
define = -DPOSRES
integrator = steep
emtol = 10
nsteps = 1500
nstenergy = 1
energygrps
> On 26/07/2012 6:47 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Ho,
>> first I minimize my structure. This is the corresponding mdp file:
>>
>> define = -DPOSRES
>> integrator = steep
>> emtol = 10
>> nsteps = 1500
>> nstenergy
Hi Mark,
>You're not the first to make this wrong assumption, but GROMACS actually
>exchanges coordinates among (sets of) cpus, which write to the same
>output file, i.e. the trajectories written by mdrun are already at
>constant temperature. (That's inefficient because you have to re-do the
>
Dear gmx users
I did the simulations of carbon nanotube+surfactant+water molecules and I
would like to calculate probability distribution of the angle formed
between the vector of the surfactant molecules and CNT. Is there any
tools or programs in gromacs to do that?I have tried g_sgangle program b
Dear gmx users,
I am using template.c of gromacs 4.0.7 for writing my own analysis
tool. When I am using the fr.x[i][XX], it writes the coordinates of
the particles (i crosschecked it with the coordinates written by the
trjconv command). But the problem arises when I use fr.v[i][XX] for
writing th
Dear Gromacs users,
Is it easily possible to calculate the number of H-bonds per molecule across
the box by using gromacs? If it is, how can I do this?
Thanks in advance,
Akn.
--
View this message in context:
http://gromacs.5086.n6.nabble.com/H-bonds-per-molecule-across-the-box-tp499969
On 7/26/12 6:07 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 26/07/2012 6:47 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Ho,
first I minimize my structure. This is the corresponding mdp file:
define = -DPOSRES
integrator = steep
emtol
On 7/26/12 3:55 AM, neeru sharma wrote:
Dear Gromacs users,
I have a query regarding the number of bins used in wham analysis.
If I have performed by simulations over 15 umbrellas (15 different
staring structures), what should be the ideal number of bins to
perform wham analysis? Does it depe
On 7/26/12 6:23 AM, akn wrote:
Dear Gromacs users,
Is it easily possible to calculate the number of H-bonds per molecule across
the box by using gromacs? If it is, how can I do this?
One would have to use g_select on a particular region of the box (simple
coordinate boundaries) to work wit
On 26/07/2012 8:22 PM, prithvi raj pandey wrote:
Dear gmx users,
I am using template.c of gromacs 4.0.7 for writing my own analysis
tool. When I am using the fr.x[i][XX], it writes the coordinates of
the particles (i crosschecked it with the coordinates written by the
trjconv command). But the p
True, I found the lower bin numbers makes the error change (increase),
especially at ends of the run, howevere the mean values were the same. I also
checked with g_sham as comparision, and found again the means the same but
differences in error (max and min values if I include all data). So a
Thanks for the clarification.
Forgot that virtual sites have no mass. With this info it is clear why a
setup with 2 'normal' and one dummy atom would not work.
Am 26.07.2012 01:42, schrieb gmx-users-requ...@gromacs.org:
On 26/07/2012 4:12 AM, Broadbent, Richard wrote:
>Virtual sites are by d
>
>
> On 7/26/12 6:07 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>>> On 26/07/2012 6:47 PM, reising...@rostlab.informatik.tu-muenchen.de
>>> wrote:
Ho,
first I minimize my structure. This is the corresponding mdp file:
define = -DPOSRES
integra
On 26/07/2012 8:17 PM, ppxasjsm wrote:
Hi Mark,
You're not the first to make this wrong assumption, but GROMACS actually
exchanges coordinates among (sets of) cpus, which write to the same
output file, i.e. the trajectories written by mdrun are already at
constant temperature. (That's inefficie
Thanks Justin for your reply.
I did see that the default bins value is 200, but I was not sure what does
it signify. It says " no of bins used in the analysis".
That's why I was confused whether it is equal to no. of umbrella sampling
simulations we run and give input to g_wham.
Thanks for cleari
On 7/26/12 7:06 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 7/26/12 6:07 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 26/07/2012 6:47 PM, reising...@rostlab.informatik.tu-muenchen.de
wrote:
Ho,
first I minimize my structure. This is the corresponding mdp file:
On 26/07/2012 9:06 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 7/26/12 6:07 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 26/07/2012 6:47 PM, reising...@rostlab.informatik.tu-muenchen.de
wrote:
Ho,
first I minimize my structure. This is the corresponding mdp file:
Thanks Stephan for you suggestion.
I will try the analysis with larger value of bins.
--Neeru
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Bins-in-wham-analysis-tp4999648p4999709.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mai
Thanks again!
Being able to read helps i guess.
Antonia
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Problem-with-REMD-tp4999684p4999711.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing listgmx-users@gromacs.org
http://l
On 26/07/2012 9:21 PM, Arunima Kumar wrote:
Dear Sir
I am Arunima Kumar Verma..a researcher from India. I found your
email id from mailing list mentioned in GROMACS.
Then you will have seen there the frequent requests from people not to
make personal requests for help on general GROMAC
On 26/07/2012 8:21 PM, niaz poorgholami wrote:
Dear gmx users
I did the simulations of carbon nanotube+surfactant+water molecules and I
would like to calculate probability distribution of the angle formed
between the vector of the surfactant molecules and CNT. Is there any
tools or programs in gr
>
>
> On 7/26/12 7:06 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>>>
>>>
>>> On 7/26/12 6:07 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
> On 26/07/2012 6:47 PM, reising...@rostlab.informatik.tu-muenchen.de
> wrote:
>> Ho,
>> first I minimize my structure. T
Quite sure it's just different syntax in topology and mdp file. Compare to C;
#define POSRES // expressed as -DPOSRES in the mdp file
#ifdef POSRES // when working in the topology file
// Linus
On Thu, Jul 26, 2012 at 1:52 PM,
wrote:
>>
>>
>> On 7/26/12 7:06 AM, reising...@rostlab.informatik.tu-
Hmm, okey. Thank you.
So all in all what I did was correct and it should only minimize the
hydrogen atoms and not the rest of the protein nor the membrane. Right?
> Quite sure it's just different syntax in topology and mdp file. Compare to
> C;
> #define POSRES // expressed as -DPOSRES in the mdp
On 7/26/12 7:52 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 7/26/12 7:06 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 7/26/12 6:07 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
On 26/07/2012 6:47 PM, reising...@rostlab.informatik.tu-muenchen.de
wrote
On 7/26/12 8:05 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hmm, okey. Thank you.
So all in all what I did was correct and it should only minimize the
hydrogen atoms and not the rest of the protein nor the membrane. Right?
To sum up:
1. The Protein-H group does indeed contain on
Dear Gromac's users!
I have some questions about simulation of the membrane protein
complexed with it's ligand in the membrane environment.
1- I want to simulate number of such similar systems ( e.g protein in
POPC bilayer) which differs only in ligand complexed into protein
interiour. Should I
On 26/07/2012 10:14 PM, James Starlight wrote:
Dear Gromac's users!
I have some questions about simulation of the membrane protein
complexed with it's ligand in the membrane environment.
1- I want to simulate number of such similar systems ( e.g protein in
POPC bilayer) which differs only in l
Hi okey,
thank you!!
>
>
> On 7/26/12 8:05 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hmm, okey. Thank you.
>> So all in all what I did was correct and it should only minimize the
>> hydrogen atoms and not the rest of the protein nor the membrane. Right?
>>
>
> To sum up:
>
> 1. Th
Dear All,
While running minimization I imposed the the condition for the
minimization as to be converged only at Fmax < 10 . But I got the
following
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
Double precision normally
Thanks Dr. Abraham
sorry for my unawareness about proper use of distance restraints. running
new MD with some modifications in mdp and top file.Hope it would work.
with best regards
Priyanka Shah
--
View this message in context:
http://gromacs.5086.n6.nabble.com/distance-restraints-around-Zn-
On 7/26/12 8:30 AM, tarak karmakar wrote:
Dear All,
While running minimization I imposed the the condition for the
minimization as to be converged only at Fmax < 10 . But I got the
following
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested
Plz be very specific about your problem. In fact iam not able to find
out that problem is.
what is the error msg
what did you do
do you need a sge script to submit job in a super computer or a
cluster??? if so then what queing system all thes ethings are very imp
On Thu, Jul 26, 2012 at 7:33 AM,
Mark,
> Only if the apo form has room for you to cut and paste in all your
> ligands... You'll have to equilibrate independently in each case, so you
> don't gain anything by not creating the system from the beginning each time.
This can gain in terms of avoiding of time-consumptions solvation
Dear Mark
thank you for your concern.when I tried the g_sgangle program
it gave me
Fatal error:
Something wrong with contents of index file.
the index file was the one I used during the simulation and I made that
with this command:
make_ndx -f em.gro -o index.ndx
and the groups for temperature coup
On 7/26/12 9:48 AM, niaz poorgholami wrote:
Dear Mark
thank you for your concern.when I tried the g_sgangle program
it gave me
Fatal error:
Something wrong with contents of index file.
the index file was the one I used during the simulation and I made that
with this command:
make_ndx -f em.gro
Dear all,
I am getting a nan while calculating the overlap between covariance matrices
(in this case, using the same vectors for -v and -v2):
g_anaeig455 -v atp/eigenvectors.trr -v2 atp/eigenvectors.trr -over
overlap_atp-atp
I tried different gromacs versions, different -last values, and als
On 27/07/2012 12:31 AM, Joaquim Rui de Castro Rodrigues wrote:
Dear all,
I am getting a nan while calculating the overlap between covariance matrices (in this case, using the same vectors for -v and -v2):
g_anaeig455 -v atp/eigenvectors.trr -v2 atp/eigenvectors.trr -over
overlap_atp-atp
I
Hi all,
To check a topology, is it correct to compare topologies generated by 2
different force fields? For example with gmx and charmm36. I know the topology
generated by gmx is correct, however the parameters might be different.
Thanks in advance .
Sincerely,
Shima
--
gmx-users mailing li
On 2012-07-26 22:09, Shima Arasteh wrote:
Hi all,
To check a topology, is it correct to compare topologies generated by 2
different force fields? For example with gmx and charmm36. I know the topology
generated by gmx is correct, however the parameters might be different.
You can not compare
Just for future reference, this feature is no longer functional and hasn't been
developed/updated to 4.5.5
If someone wants to use it, then will either have to use an older version of
GROMACS where it is still working (yet to pin that down, but when I do will
note which is the latest one in whi
Hi,
I would like to extend a run. I ran a 10 ns simulation, and I would like to
run the simulation for an additional 10 ns. Normally I would do this with
the following two commands:
tpbconv -s topol_old.tpr -o topol_new.tpr -extend 1
mdrun -cpi checkpoint_old.cpt -s topol_new.tpr -noappend
On 7/26/12 9:59 PM, Andrew DeYoung wrote:
Hi,
I would like to extend a run. I ran a 10 ns simulation, and I would like to
run the simulation for an additional 10 ns. Normally I would do this with
the following two commands:
tpbconv -s topol_old.tpr -o topol_new.tpr -extend 1
mdrun -cpi
Hi,
Just read,
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions.
But could not get it.
Please suggest hoe to fix the visual issues with the molecule being broken into
two parts in the final simulation.
Thanks in advance.
Radhika
--
gmx-users mailing listgmx-us
On 27/07/2012 2:08 PM, radhika jaswal wrote:
Hi,
Just read,
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions.
But could not get it.
Please suggest hoe to fix the visual issues with the molecule being broken into
two parts in the final simulation.
There's a sugge
55 matches
Mail list logo
