Hi Rajat,
If you remove comm on the bilayer, there may be relative comm between
leaflets. If that relative motion is significant and you switch to removing
comm per leaflet, the program suddenly finds itself resetting the com over
a large distance. About equilibration, you equilibrated with
Hi,
Something went wrong earlier in your workflow. Check your log files, etc.
Mark
On Nov 13, 2013 3:57 AM, guozhicheng222 guozhicheng...@126.com wrote:
Hi:
When I am running the ibi procedure, I get the following error message:
A coordinate in file
Hi Tsjerk,
That was very sage advice! Thank you. I will try regenerating velocities
and see if the motion goes away...
On Wed, Nov 13, 2013 at 2:00 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Rajat,
If you remove comm on the bilayer, there may be relative comm between
leaflets. If that
An update to anyone interested:
Regenerating velocities by itself did not solve the problem. I had to
regenerate velocities and couple the upper and lower leaflets separately to
the thermostat to equilibrate the system. To smoothen the equilibration
process further, I used a 0.5 fs timestep
Dear Justin
Very thanks for your reply.
I created a new topol.top file as below:
1) I used once default directive.
2) I put cnt.itp file in working directory.
3) I copied pr.top and renamed it to topol.top. I added #include cnt.itp
in the end of topol.top file. I modified [ molecules ]
Hello GROMACS users,
I have phosphorylated Serine residue in my
protein (140 residues) of interest, now when I run pdb2gmx I get this
following error
Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms
while sorting atoms.
I checked
Dear Justin
My cnt is infinite.
I obtained cnt.top by g_x2top and then modified cnt.top to cnt.itp.
For obtaining cnt.top, I used following files:
---
ffcnt.atp:
CA 12.01100 ; aromatic C
Hello Mark,
I don't get any informing of your reply by e-mail, but get your reply
searched by google.
Anyway thanks very much for your reply!
Yeah, I used two totally different mdp files for the single point
calculation because I thought
that gromcs would report the potential energy of my
Dear All,
can anyone tell me how to construct mixed lipid bilayer in gromacs
id possible also provide me the command to construct the mixed bilayer
Thanks in advance
Nikhil
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Hello, all
I intend to make some modification on minimize.c in mdlib.
Do I need to do cmake make make install all over again?
Or is there a quick way for recompiling?
Thanks for any tips.
JhengWei Li
Institute of Atomic and Molecular Sciences,
Academia Sinica, Taipei 106, Taiwan
--
gmx-users
On 11/13/13 12:20 AM, Venkat Reddy wrote:
Dear Justin and Piggot,
Thanks for the suggestions. Actually, I have constructed a CG lipid vesicle
by placing lipids in random conformation in a simulation box. My lipid
system is heterogeneous, i.e., it has different types of lipids
On 11/13/13 5:51 AM, Atila Petrosian wrote:
Dear Justin
Very thanks for your reply.
I created a new topol.top file as below:
1) I used once default directive.
2) I put cnt.itp file in working directory.
3) I copied pr.top and renamed it to topol.top. I added #include cnt.itp
in the end of
On 11/13/13 6:02 AM, hasthi wrote:
Hello GROMACS users,
I have phosphorylated Serine residue in my
protein (140 residues) of interest, now when I run pdb2gmx I get this
following error
Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms
while
Start with packmol if you want to start from scratch. Or else get a pretty
equilibrated mixed lipid bilayer if available somewhere on web.
On Nov 13, 2013 6:45 PM, Nikhil Agrawal nikhil.08...@gmail.com wrote:
Dear All,
can anyone tell me how to construct mixed lipid bilayer in gromacs
id
Hi Nikhil,
The first step would be to determine what forcefield you are going to use
for the lipids. If you are going to use Charmm or Slipids, you can use
charmmgui (just google it). If you are planning to use the Gromos
forcefields, you can check Prof. Tieleman's website or lipidbook for pure
Let me correct myself :). Its pre-equilibrated. Not pretty equilibrated. :)
On Nov 13, 2013 7:23 PM, Arun kumar V arun.tar...@gmail.com wrote:
Start with packmol if you want to start from scratch. Or else get a pretty
equilibrated mixed lipid bilayer if available somewhere on web.
On Nov 13,
For just modifying a file, just doing make is sufficient. I would
recommend not installing the modified version (since you can run the
build/src/kernel/mdrun directly), or if you must install, to use the
suffixing options available in the ccmake advanced mode.
Mark
On Nov 13, 2013 2:48 PM, Jheng
Probably the default behaviour of pdb2gmx for termini is not appropriate
for your input. Use pdb2gmx -ter and choose wisely
Mark
On Nov 13, 2013 12:03 PM, hasthi durgs7kr...@gmail.com wrote:
Hello GROMACS users,
I have phosphorylated Serine residue in my
protein
Dear Justin,
I have referred to an article (Vuorela T, Catte A, Niemela PS, Hall A,
Hyvonen MT, et al. (2010) Role of Lipids in Spheroidal High Density
Lipoproteins. PLoS Comput Biol 6(10): e1000964.
doi:10.1371/journal.pcbi.1000964), where the authors have clearly described
the fitting of 2D
On 11/13/13 9:41 AM, Venkat Reddy wrote:
Dear Justin,
I have referred to an article (Vuorela T, Catte A, Niemela PS, Hall A,
Hyvonen MT, et al. (2010) Role of Lipids in Spheroidal High Density
Lipoproteins. PLoS Comput Biol 6(10): e1000964.
doi:10.1371/journal.pcbi.1000964), where the authors
Dear Justin
Thanks for your reply.
In your previous setup, you were effectively trying to use CHARMM27 + some
other
force field related to the CNT. You can't do that.
Thus, Gromacs is not appropriate for systems containing cnt.
Is my deduction true?
In my case, peptid + cnt + water
On 11/13/13 10:39 AM, Atila Petrosian wrote:
Dear Justin
Thanks for your reply.
In your previous setup, you were effectively trying to use CHARMM27 + some other
force field related to the CNT. You can't do that.
Thus, Gromacs is not appropriate for systems containing cnt.
Is my deduction
Dear Justin
Thanks for your quick reply.
I was confused.
If I add #include ffcntbon.itp after #include cnt.itp in .top file,
my problem was solved and error was solved?
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On 11/13/13 11:53 AM, Atila Petrosian wrote:
Dear Justin
Thanks for your quick reply.
I was confused.
If I add #include ffcntbon.itp after #include cnt.itp in .top file,
my problem was solved and error was solved?
No. The parameters are at the force field level and thus have to be
Hi GROMACS users,
GROMACS 4.6.4 is officially released. It contains numerous bug fixes, and
some noteworthy simulation performance enhancements (particularly with
GPUs!). We encourage all users to upgrade their installations from earlier
4.6-era releases.
You can find the code, manual, release
Will a simulation from 4.6.1 continue running fine if I upgrade to 4.6.4?
Hi GROMACS users,
GROMACS 4.6.4 is officially released. It contains numerous bug fixes, and
some noteworthy simulation performance enhancements (particularly with
GPUs!). We encourage all users to upgrade their
Hello,
I am trying to run MPI, OpenMP and CUDA enable GROMACS 4.6.3 on nodes having 12
cores (2 CPUs) and 2 GPUs (Tesla M2090) each. The problem is when I launch job
GROMCAS is using only GPUs on first node come across and failing to use GPUs on
other nodes.
The command I used for two gpu
sir,
I have a basic doubt about remd simulation. In remd is it possible to
run 16 replicas in 8 processors?
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sir,
I have a basic doubt about remd simulation. In remd is it possible to
run 16 replicas in 8 processors?
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Dear users,
g_energy -f *.edr -vis
I have two questions about the results of eviscoi.xvg ( derivative of
Einstein relation):
1.) I dont understand the unit of y-axis. It is kg.m^(-1).s^(-1).10^(-3) in
B.Hess 2002
In eviscoi.xvg
@yaxis label (kg m\S-1\N s\S-1\N ps)
That is
The unit of
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