Dear All,
I need a suggestion related to simulation of peptide-membrane system.
Are CGenFF parameters (from ParamChem) for peptide analogues good enough to
couple with Charmm36 parameters for the lipids in a membrane? (provided
very low charge and param penalties)
Thanks,
Tarak
--
Gromacs Users
Hi,
That suggests that your source tree is dirty, somehow. Unpack a fresh
tarball and try again.
Mark
On Tue, Feb 3, 2015 at 2:33 PM, Jim Tuccillo tucci...@sgi.com wrote:
Hi Folks,
I am seeing the following problem with a 5.0.4 build. I see that others
have had this issue also but I
Hello Mark,
I have tested both models in simulating a variety of properties. The
original parametrization results involved predicting the critical point of
CO2 and also density at various P and T. I did several NVT simulations to
predict density-vs-pressure data. In this case the model with
Hi,
With which set of parameters are you able to reproduce the original
parametrization results?
Mark
On Tue, Feb 3, 2015 at 8:04 AM, sujithkakkat . sujithk...@gmail.com wrote:
Dear all,
I tried simulating the CO2-water mixture with CO2 at a low
concentration (0.003 mole fraction) at
On 2/3/15 3:56 AM, sujithkakkat . wrote:
Hello Mark,
I have tested both models in simulating a variety of properties. The
original parametrization results involved predicting the critical point of
CO2 and also density at various P and T. I did several NVT simulations to
predict
Hi Folks,
I am seeing the following problem with a 5.0.4 build. I see that others have
had this issue also but I haven't seen a solution. Any thoughts on how to
address this? Thanks.
The build is with the following:
cmake .. -DGMX_DOUBLE=ON -DGMX_SIMD=sse4.1 -DCMAKE_C_COMPILER=gcc
Hi,
I trying to learn REMD following the tutorial on gromacs page
http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham,_Session_1B
on
a 4-cores computer.
However when I try to use the command:
On 2/3/15 2:16 PM, Stephen P. Molnar wrote:
Ok. I understand the replys.
I only have a couple of further questions.
A link to grompp is in /usr/local/gromacs/bin.
Why isn't ions.mdp in the run directory and then, where is it?
You download it from the tutorial site.
Ok. I understand the replys.
I only have a couple of further questions.
A link to grompp is in /usr/local/gromacs/bin.
Why isn't ions.mdp in the run directory and then, where is it?
Thanks in advance.
On 02/02/2015 12:29 PM, HANNIBAL LECTER wrote:
It just means you either missed grompp
Hey all,
I have been reading many post about this issue, but still do not have a
clear answer.
I am using the AMBER force-field where 1-4 interactions are scaled (fudgeLJ
= 0.5 and fudgeQQ = 0.8333).
In addition I use parameters of molecules that require the 1-4 interaction
to NOT be scaled.
On 02/03/2015 02:30 PM, Justin Lemkul wrote:
On 2/3/15 2:16 PM, Stephen P. Molnar wrote:
Ok. I understand the replys.
I only have a couple of further questions.
A link to grompp is in /usr/local/gromacs/bin.
Why isn't ions.mdp in the run directory and then, where is it?
You download
Dear Gromacs User,
I am new in Gromacs. I want to create rectangular box like dimensions 5.0
5.0 15.0 and want to put nonane-water-nonane on it. I mean there layers
first nonane and water and again nonane layers.
Would you please give some idea how to do it.
Thank you
--
Gromacs Users mailing
On 2/3/15 8:32 PM, Bishnu Acharya wrote:
Dear Gromacs User,
I am new in Gromacs. I want to create rectangular box like dimensions 5.0
5.0 15.0 and want to put nonane-water-nonane on it. I mean there layers
first nonane and water and again nonane layers.
There aren't two nonane layers,
Thank you very much for your suggestion.
On Tue, Feb 3, 2015 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/3/15 8:32 PM, Bishnu Acharya wrote:
Dear Gromacs User,
I am new in Gromacs. I want to create rectangular box like dimensions 5.0
5.0 15.0 and want to put
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