Dear Gmx-Users
Currently i'm having this kind of sticky warning when i am doing gmx solvate or
gmx editconf (ff was charmm and oplsa). However i copied vdwradii.dat in my
working directory, or use -vdwread flag still get this warning..Please how to
get rid off of this Warning!
WARNING:
Dear Gmx-Users
Currently i'm having this kind of sticky warning when i am doing gmx solvate or
gmx editconf (ff was charmm and oplsa). However i copied vdwradii.dat in my
working directory, or use -vdwread flag still get this warning..Please how to
get rid off of this Warning!
WARNING:
Dear Gmx-Users
Currently i'm having this kind of sticky warning when i am doing gmx solvate or
gmx editconf (ff was charmm and oplsa). However i copied vdwradii.dat in my
working directory, or use -vdwread flag still get this warning..Please how to
get rid off of this Warning!
WARNING:
ct: Re: [gmx-users] gmx convert-tpr, gmx check Q ?
On 4/12/16 8:16 AM, badamkhatan togoldor wrote:
> Dear GMX-Users,I have a technical question regarding to the gmx convert-tpr
> and gmx check. I have a little bit doubt in that. Simulation was
> calculating 5.000.000 steps, 10ns and it
Dear GMX-Users,I have a technical question regarding to the gmx convert-tpr and
gmx check. I have a little bit doubt in that. Simulation was calculating
5.000.000 steps, 10ns and it has stopped due to the some cluster time limit. So
I want to continue it from that stopped step. So,
gmx
Dear GMX-Users,I have a technical question regarding to the gmx convert-tpr and
gmx check. I have a little bit doubt in that. Simulation was calculating
5.000.000 steps, 10ns and it has stopped due to the some cluster time limit. So
I want to continue it from that stopped step. So,
gmx
Dear Gmx-Users,
I had done roughly 300ns peptide and membrane simulation. I am trying to do
some analyses through the do_dssp. To get in .xpm file I put .xtc and .tpr
files. Then at certain frame its just killed and gave me the empty files with
strange names like ddccTf1j, ddmMD9pt,
Dear GmxUsers,
Recently I got this Note in my enegy minimization (l-bfgs) step. I am using
5.1.1 version.
You are using geometric combination rules in LJ-PME, but your non-bonded C6
parameters do not follow these rules. This will introduce very small errors in
the forces and energies in
I think i've just found my mistake. Thank you so much again.
Khatnaa
On Friday, 30 October 2015, 18:55, Justin Lemkul <jalem...@vt.edu> wrote:
On 10/30/15 7:09 AM, badamkhatan togoldor wrote:
> Thank you Justin.
>> The better question is why you're trying to dec
4, Justin Lemkul <jalem...@vt.edu> wrote:
On 10/29/15 4:56 AM, badamkhatan togoldor wrote:
> Dear GMX Users, I am simulating a free energy of a protein chain_A in water
> by parallel. Then i got domain decomposition error in mdrun. Will use 15
> particle-particle and 9 PME o
Dear GMX Users,
I am simulating a free energy of a protein chain_A in water by parallel. Then i
got domain decomposition error in mdrun.
Will use 15 particle-particle and 9 PME only ranksThis is a guess, check the
performance at the end of the log file
Dear Gmx Users,
I have a question on grompp !
I built some membrane in Charmm-gui with ion and water etc and i took that
output data for gromacs. Then i changed .pdb file on the gromacs. Do the
pdb2gmx and editconf then grompp. Unfortunately grompp gave me an error!
No default U-B
Dear GMX userI got following error on the membeding process.Then i have to
change my box type in here?
and also XTC error : I have to run it more bigger machine?
Warning: Only triclinic boxes with the first vector parallel to the x-axis and
the second vector in the xy-plane are supported.
Dear Gromacs Users,I would like to use g_membed to insert my peptide into
membrane. But I got this errors and notes in grompp
ERROR 1 [file membed.mdp]:
Energy group exclusions are not (yet) implemented for the Verlet scheme
NOTE 4 [file membed.mdp]:
NVE simulation with an initial
Hi,i’m following KALP-15 in DPPC tut in my own peptide (novel) and lipid
(pope). I created charm27_lipid.ff for my lipid. In this case i should create
for such ff to my lipid or it’s necessary to create? Then its gave me fatal
error on grumpTopology include file "gb.itp" not foundWhere i have
Hi,i’m following KALP-15 in DPPC tut in my own peptide (novel) and lipid
(pope). I created charm27_lipid.ff for my lipid. In this case i should create
for such ff to my lipid or it’s necessary to create? Then its gave me fatal
error on grommpTopology include file "gb.itp" not foundWhere i have
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