Hi,Dear users and JustinI want to perform MD simulations on gold nanoparticles
and have a couple of questions to ask. For example I want to equilibrate a gold
nanoparticle in a box of solvent. As I went through the existing data on the
Internet I found nothing on this issue. Now, Is Gromacs
Hi everyone,
I am trying to run a simulation of a lipid bilayer with a multi-component
solution. One of the components is ethylene glycol. Some of the components have
a tendency to wriggle their way into the lipids. When an EG molecule does this,
it tends to get uncomfortable and trigger some
I have parameters for 8-oxoguanine in FRCMOD and PREP files. Adding
information from .prep file to dna.rtp an creating a modified entry in
dna.hdb is simple enough.
However I'm stuck now translating bond and angle data from .frcmod to
.itp file, as its notation system is very different and its
Hi Mark,
I'll give it a shot and see. One other thing I forgot to mention is that the
first EG topology has been successfully used for membrane simulations in
GROMACS 3.3.3 using SHAKE. I am continuing this work but wanted to use GROMACS
4.6.7 to speed things up. Unfortunately GROMACS 4.6.7
Hi,
While we can't exclude the possibility of a code bug, your analysis and
results suggest the problem lies elsewhere. Is the EG model stable if you
e.g. put one in a box of decane? It's a stab in the dark, but if EG was
parameterized only for aqueous-phase properties, then all bets are off once
I wish I could offer some help. br/I used to prepare small compound
molecules, and the ligand.frcmod was generated by parmchk of AMBER. The
ligand.frcmod was then handed to tleap or xleap of AMBER, to generate
ligand.prmtop and ligand.inpcrd. Following that, a python script called
acpype.py
I'm curious what are the conditions under which you get such a exceptional
speedup. Can you share your input files and/or log files?
--
Szilárd
On Thu, Jul 2, 2015 at 2:18 AM, Alex nedoma...@gmail.com wrote:
Yup, about 7-8 times between with and without GPU acceleration, not making
this up: I
Hi,
I've tried to set up implicit solvent simulations in Gromacs 5.0.2. It
is recommended that one uses PBC=no and infinite cutoffs for implicit
solvent (GBSA) simulations. However, if I use the Verlet cutoff
scheme, grompp throws an error, saying that Verlet doesn't support
PBC=no. If I use
I could be mixing something up, so let me double check before sharing inputs.
Alex
I'm curious what are the conditions under which you get such a exceptional speedup. Can you share your input files and/or log files?
--
Szilárd
On Thu, Jul 2, 2015 at 2:18 AM, Alex
On 7/2/15 7:16 AM, Timofey Tyugashev wrote:
I have parameters for 8-oxoguanine in FRCMOD and PREP files. Adding information
from .prep file to dna.rtp an creating a modified entry in dna.hdb is simple
enough.
However I'm stuck now translating bond and angle data from .frcmod to .itp file,
as
Hi,
You could also observe the change in e.g. free-energy of solvation of that
ion in that force field upon change in temperature. Or maybe something even
more relevant?
Mark
On Thu, Jul 2, 2015 at 5:29 PM Justin Lemkul jalem...@vt.edu wrote:
On 7/2/15 10:33 AM, soumadwip ghosh wrote:
Hi,
Hi,
I am stuck with one of the reviews of my paper where i have
investigated the thermodynamics of small molecular ion binding to DNA
duplex using CHARMM 27 force field. In order to do so I calculated the PMF
of the binding processes at different temperature ( 300, 270 and 330K) and
then
Hi,
That is indeed a current limitation. There's plans to make infinite cutoffs
possible before we remove the group scheme. Not sure if there is draft code
yet.
The implicit solvation code, even in the group scheme has had essentially
no testing since 4.6 (e.g. search the archives for other such
On 7/2/15 10:33 AM, soumadwip ghosh wrote:
Hi,
I am stuck with one of the reviews of my paper where i have
investigated the thermodynamics of small molecular ion binding to DNA
duplex using CHARMM 27 force field. In order to do so I calculated the PMF
of the binding processes at different
Szilárd,
I was wrong. When I run with GPU and use -ntomp 4, I have 400% CPU
utilization and that yields about 83 ns/day. When I do -ntomp 4 -nb cpu, I
get 1600% CPU utilization and get similar results.
However, when I run -nt 4 -nb cpu, I get 400% CPU utilization, and then it
is slower. I am
Dear Gromacs users,
I have problem in running final step
(md.mdp). i ran the job as nsteps=5000, dt=0.002, it is for 10 PS level.
it runs properly. After that i increased the values nsteps= 5, 50
dt =0.002, (that means 100 PS , 1000 PS) in md.mdp
Hi,
You need to rerun grompp with revised .mdp file to generate a new .tpr file
for you new, longer runs. mdrun doesn't interact with .mdp file directly.
Regards
Terry
On Fri, Jul 3, 2015 at 9:57 AM, Sivanandam M sivanandam...@gmail.com
wrote:
Dear Gromacs users,
Hello Gromacs users,
I have run several 50 ns production runs using Gromacs. Can anyone tell me how
to calculate interaction energy of indvidual protein residues with ligand? I
had set energygrps as Protein LIG (LIG for ligand). I have gone through the
archives, but these do not tell much and
Dear Gromacs users,
I am working with membrane proteins. I have build my membrane-protein
systems with a layer of water bed on top and bottom of the membrane. Now,
I would like to add a specific concentration of KCl to bottom layer of the
water bed. Can anybody suggest me a way to add ions to a
Dear users,
I want to uninstall gromacs. I used this command: rm -rf /usr/local/gromacs
and also removed some links that began with g_*** in the bin . however, I'm
not sure if the rest belong to gromacs or other programs also use them, and
should be deleted or not: completion.bash,
Dear Justin and Mark,
I have written a reply to the reviewer
where I have mentioned the works ( DPPC membrane, protein unfolding
and so on) where different objectives have been met with upon varying
concentrations and it seems that the force fields just do fine. The
Hi,
Dunno, never tried the walls code.
Mark
On Thu, Jul 2, 2015 at 11:37 PM João Martins joaomartins...@gmail.com
wrote:
As a completely pointless point since Mark just explained why it doesn't
make much sense to do it, you can achieve the same by separating your
waters in the [ molecules ]
Here's for the CPU-only run:
R E A L C Y C L E A N D T I M E A C C O U N T I N G
On 1 MPI rank, each using 4 OpenMP threads
Computing: Num Num CallWall time Giga-Cycles
Ranks Threads Count (s) total sum%
Hi,
Your membrane is probably in the x-y plane, so you just insert ions
everywhere and delete from the .gro file all that have a z coordinate
bigger than whatever value aligns with the bottom of your membrane, and
correct the number of atoms in the .gro and .top file accordingly.
This won't help
Hi,
The functional forms available are in chapter 4 of the reference manual,
and the way to specify the parameters is in chapter 5. So perhaps after
some trig, you should be good to work that out (if not, then tabulated
bonded interactions are also possible). Make a trivial test case whose
energy
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