Hi,
I am a newer to GROMACS. I want to simulate the CO2 + Water + Surfactant
system with GROMACS 2019.4. I generated the .pdb file with Packmol like
below. After the 5 steps steep EM, I want to run the cg EM, but it
always had errors, One or more water molecules can not be settled.
Is it
On 2/18/20 3:57 PM, Sadaf Rani wrote:
Dear Gromacs users
I am getting the following message while running an energy minimization:-
There is no domain decomposition for 32 ranks that is compatible with the
given box and a minimum cell size of 1.85723 nm
I am not using any distance restraint,
Dear Gromacs users
I am getting the following message while running an energy minimization:-
There is no domain decomposition for 32 ranks that is compatible with the
given box and a minimum cell size of 1.85723 nm
I am not using any distance restraint, and selecting box size by the
following
http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision
On Tue, 17 Jul. 2018, 11:12 pm neelam wafa, wrote:
> Hi,
>
> Dear gromacs users, I am running md simmulation of a protein with a ligand.
Hi,
Dear gromacs users, I am running md simmulation of a protein with a ligand.
i have already done it with the same protein and a different ligand. Now
when i run em md run i get following result.
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax
Dear Justin,
I have tried to change the box size, make it smaller a little, solvate
again and then, the error is resolved. Actually, I don't understand the
reason. especially, I have no idea about the impossible geometry as you
mentioned. Can you give me a little explanation?
Thank you so much.
Hi Jin,
Can you give the protocol you used in commands? And what are the box
dimensions and how many solvent molecules were added?
Cheers,
Tsjerk
On Jun 5, 2015 08:30, Jin J.C jcjin.hcmut@gmail.com wrote:
Dear Justin,
I have tried to change the box size, make it smaller a little, solvate
Dear Justin,
My protocol is simply like this:
1. Prepare the system of protein embedded in a equilibrated pure DOPC
bilayer.
2. Make a rectangular box
gmx editconf -f protein-mem.gro -o protein-mem-box.gro -box 14.6 14.6
16.3 -center 7.3 7.3 8.15
3. solvate
gmx solvate -cp protein-mem-box.gro
On 6/3/15 10:23 PM, Jin J.C wrote:
Dear all,
I am trying to set a coarse-grained MD for the membrane protein.
After solvating, I met an error when running a short energy minimization (
10 steps) before adding ions.
Steepest Descents:
Tolerance (Fmax) = 1.0e+01
Number of steps=
Dear all,
I am trying to set a coarse-grained MD for the membrane protein.
After solvating, I met an error when running a short energy minimization (
10 steps) before adding ions.
Steepest Descents:
Tolerance (Fmax) = 1.0e+01
Number of steps= 10
Step= 10, Dmax= 2.0e-05 nm,
Hello everyone,
I am trying to energy minimize protein-ligand complex in lipid membrane. I
am using LAMBADA script, after extracting Ligand. LAMBADA script do not
recognise ligand molecule, after insertion when I am trying to reinsert
ligand in to Prot_memb system, it does not bind to protein
Hello,
I am simulating a double stranded DNA in presence of choline. I am
using CHARMM force field and GROMACS 4.5.6 for my simulations. I made the
choline molecule as suggested by justin using CGenFF and included in my
system by using -ci -nmol option of genbox. I am facing some problems
On 12/9/14 6:51 AM, soumadwip ghosh wrote:
Hello,
I am simulating a double stranded DNA in presence of choline. I am
using CHARMM force field and GROMACS 4.5.6 for my simulations. I made the
choline molecule as suggested by justin using CGenFF and included in my
system by using -ci
Hello all,
Do we need to create a box using editconf before using grompp to carry
out energy minimization between shrinking steps.???
Thanks,
Padmani
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Thanks Justin. The OGA topology is now OK. But still the problem with the
FE ion persists (very high force on it) during the minimization.
Yes, I want to link the FE with its co-ordination atoms by simple harmonic
(bond type 6), can you please tell what will be the value for kb (the force
On 6/18/14, 6:47 AM, sucharita dey wrote:
Thanks Justin. The OGA topology is now OK. But still the problem with the
FE ion persists (very high force on it) during the minimization.
Yes, I want to link the FE with its co-ordination atoms by simple harmonic
(bond type 6), can you please tell
ok, I tried with an arbitrary value of kb for all the harmonic bonds
(715) and the distances as they are in the crystal structure. There
are 5 harmonic bonds with FE which I defined in the itp, but I am getting
an error on one of them while doing position restrained MD for 50 ps. I
tried with
On 6/13/14, 2:11 AM, sucharita dey wrote:
Dear Users,
I have a protein-DNA system with 3 Zinc fingers, 1 Fe++, 1 cofactor NOG
(N-OxalyGlycine) and crystal waters.
I have generated the initial topology of OGA from PRODRG and incorporated
it in the the forcefield gromos 53a6 and since the
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