Dear Gromacs users,
I need to work with a united atom FF, but I have defined all the Hydrogens
in my pdb file. Does it cause any problem in MD procedure?
Truly yours,
Farideh
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I created the pdb file by genconf but the system was not minimized, i got
positive potential energy. What may be the problem?
On 11 Aug 2015 19:38, "Mark Abraham" wrote:
> Hi,
>
> gmx genconf on a small box with a single argon is a useful starting point.
>
> Mark
>
> On Tue, Aug 11, 2015 at 3:16
Dear Dr. Justin and Gromacs User,
Thank you so much for your helps.
When I use charmm36 ff to generate the topology for lipid (DOPC). I got
many warning "Warning :Long bond "
And after get the topology, the total charge is very high (+888 e for DOPC
bilayer have 516 molecular). When I used grompp
On 8/11/15 11:06 AM, anu chandra wrote:
Dear Justin,
Thanks for your quick reply.
I am trying to run membrane protein simulation with slab geometry and EW3DC
method (ewald-geometry = 3dc), due to ion asymmetry in the system.
Following the article
http://www.cell.com/biophysj/abstract/S0006-34
Dear all,I am simulating polarizable water with Gromacs 5.0.5. I am wondering
if it is possible to calculate the pressure profiles along z axis.I do not find
corresponding programs from the manual. Instead, I find some discussions 4
years ago from the mailing list, but they do not make much sens
Dear users,
My system contains peptide + TFE + water in an octahedron box.
I am using oplsaa.ff
I am trying to do EM but running this command
grompp -f em.mdp -c C22_TFE-W.gro -p topol.top -o em.tpr
the next error message come up
WARNING 1 [file em.mdp]:
The sum of the two largest charge gro
Hello,
I am benchmarking a new cluster and also learning the ropes of GROMACS. I
am using the dppc benchmark from
http://www.gromacs.org/About_Gromacs/Benchmarks
On the first cluster, which contains 8 processors per node, I have the
scaling one might expect
# n ranks [performance (ns/day)
Hello Michael,
I believe a non-parallel implementation is fine. Thank you for the guidance.
I am running QM/MM calculations in GROMACS over relatively short timescales
(10 ps) with a fine timestep (0.1 fs). My system follows the dynamics of
atoms with thermal and hyperthermal velocities and the l
Adding an integrator for your own work is hard but doable, especially
if you don't need it parallelized. Look at the do_update_X routines
for examples. It will be harder for 5th/6th order since you probably
need values of the forces for times in the past, which are not
automatically stored in gr
Hello GROMACS users,
I am interested in adding a fifth/sixth order predictor/corrector
integrator to GROMACS. Is this possible? If so, any guidance on which files
need to be updated is much appreciated.
Best,
Eric
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Hai gromacs users
I am trying to run the simulation of rna with
urea as solvent. I have added 300 molecules of water using genbox command
and while runnning the energy minimization step, the total potential energy
is coming as positive. please help me to solve this pro
Dear Justin,
Thanks for your quick reply.
I am trying to run membrane protein simulation with slab geometry and EW3DC
method (ewald-geometry = 3dc), due to ion asymmetry in the system.
Following the article
http://www.cell.com/biophysj/abstract/S0006-3495%2803%2974458-0?mobileUi=0
, I have set up
On 8/11/15 8:30 AM, anu chandra wrote:
Dear Gromacs users,
I am working with membrane simulations and I would like to put distance
restrain along Z-axis between a dummy atom I generated at the centre of box
and all the water molecules. For this, I first generated a dummy atom at
the centre of
On 8/11/15 10:01 AM, Vy Phan wrote:
Dear Gromacs users,
On the .itp file on the charmm36 force field, I see the DOPC and other
lipid which have the [atom][bond] and [ impropers] parameter. I wonder
where is the parameter for [dihedrals].
Angles and dihedrals are automatically generated from
Dear Gromacs users,
On the .itp file on the charmm36 force field, I see the DOPC and other
lipid which have the [atom][bond] and [ impropers] parameter. I wonder
where is the parameter for [dihedrals].
please help me!
Thank in advance
Tuong Vy
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Hi,
gmx genconf on a small box with a single argon is a useful starting point.
Mark
On Tue, Aug 11, 2015 at 3:16 PM Sunil Ghimire
wrote:
> How can i create the .pdb file for 1600 atoms of argon ?
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How can i create the .pdb file for 1600 atoms of argon ?
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Dear Gromacs users,
I am working with membrane simulations and I would like to put distance
restrain along Z-axis between a dummy atom I generated at the centre of box
and all the water molecules. For this, I first generated a dummy atom at
the centre of box and also made a simple .itp file for it
Hi,
Since bonds break and form upon proton transfer it requires quantum mechanics,
both for the electrons and the proton(s).
To avoid the heavy computational burden, one can opt to use classical dynamics
for the proton and semi-empirical methods, which are accessible in Gromacs (<5)
through t
Hello,
I want to study proton transfer reaction in a protein channel using
gromacs. I read in the literature that it is not possible to do this by
classical MD, then what are the other ways to perform it in gromacs..??
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*Research Scholar,*
*Center for Computational Biology an
Hi,
Maybe they made a mistake. You could try asking them, rather than some
strangers on the internet :-D
Mark
On Tue, Aug 11, 2015 at 5:53 AM dipak sanap wrote:
> Hi all,
>
> Thank you very much for your reply Mark, Still if i see little variation of
> few molecules here and there as explaine
On Tue, Aug 11, 2015 at 4:26 AM Bikash Ranjan Sahoo <
bikash.bioinformat...@gmail.com> wrote:
> Dear All,
>
> I want to simulate my protein in 85 and 15 % water and TFE, respectively.
>
Start simpler. Make sure you can simulate pure water, and water-TFE mixture
first. One of your problems right n
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