Hi,
"3000 water molecule per lipids per second" corresponds to 0.000384 water
molecules transferred across the membrane per nano second (assume the system
contains 128 lipids). It seems water translocation should not be observed in a
simulation of 10 ns, but I am not sure. And I only find one r
Dear all,
I want to get the PMF of my peptide across the membrane bilayer. First I pulled
my peptide across the membrane and then did windowed umbrella sampling along
the
reaction coordinates which is the z-distance between peptide and membrane.
However, I found that sampling is not sufficient
GROMACS users
Sent: Tuesday, 22 February 2011 09:35:37
Subject: Re: [gmx-users] Can g_wham support using different temperature for
different windows?
Jianguo Li wrote:
> Dear all,
>
> I want to get the PMF of my peptide across the membrane bilayer. First I
> pulled
>my peptide acro
09:58:36
Subject: Re: [gmx-users] Can g_wham support using different temperature for
different windows?
Jianguo Li wrote:
> Thanks Justin.
> I tried your suggestions by either increase more windows and change the force
>constant, but it seems the samplings are still bad in some windo
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Tuesday, 22 February 2011 11:13:05
Subject: Re: [gmx-users] Can g_wham support using different temperature for
different windows?
Jianguo Li wrote:
> Thanks for your comments, Justin.
>
> Using timestep of
ianguo
From: Jianguo Li
To: jalem...@vt.edu; Discussion list for GROMACS users
Sent: Tuesday, 22 February 2011 14:27:34
Subject: Re: [gmx-users] Can g_wham support using different temperature for
different windows?
Thanks Justin and Chris and sorry for con
windows.
Cheers
Jianguo
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Tuesday, 22 February 2011 21:10:08
Subject: Re: [gmx-users] Can g_wham support using different temperature for
different windows?
Jianguo Li wrote:
> Thanks Justin and C
lices up to 8 us ... and no charges were involved.
This might be a lot pessimistic but you should not get fooled by a CG model.
Martini is really good for a lot of things but other things should really but be
looked at carefully.
XAvier.
On Feb 22, 2011, at 9:12 AM, Jianguo Li wrote:
Sorry I fo
temperature for
different windows?
Jianguo Li wrote:
> Thank you, Justin.
> Actually I did windowed umbrella simulations from d=-1.05nm to d=9nm. Since I
>think there is no problem in the region out of the membrane, so I only show
>the
>configurations within the membrane. My objectiv
l
conformation (e.g. 10.1016/j.bpj.2010.12.3682). It is anyway a very difficult
problem (and probably impossible at atomistic resolution) to get a converged
PMF
for a whole peptide (e.g. 10.1016/j.bpj.2009.03.059).
Ciao,
Patrick
Le 23/02/2011 05:25, Jianguo Li a écrit :
> Sorry, why do you
Sent: Wednesday, 23 February 2011 20:59:18
Subject: Re: [gmx-users] Can g_wham support using different temperature for
different windows?
On Feb 23, 2011, at 3:21 AM, Jianguo Li wrote:
>Thank you for the the useful information, XAvier.
>My peptide is highly positively charged, 18 AA wi
Dear all,
I'd like to do folding simulations of a short peptide on membrane surface using
REMD using atomistic FF. But the problem is that membrane will disrupt at high
temperatures. To maintain the membrane structure, I am thinking the following
two methods:
(1) To use different coupling temp
My way of doing it is:
(1) add two new residues entries (with two different names) for glycine and
seine in the rtp file and corresponding FF files. The new entries in the rtp
file for glycine and serine should have the same number of atoms as in the
real
molecule (delete the unnecessary H o
You don't use qsub or bsub?
usually you should submit a script file containing the gromacs command, then
bsub/qsub will allocate the required resource to your job.
Jianguo
From: mohsen ramezanpour
To: Discussion list for GROMACS users
Sent: Tuesday, 8 March
I met the same problem when using 4.5.1 for some systems, the PMF shows zero
curve, while the hist file looks fine. The problem disappears when using 4.5.2.
Jianguo
From: Susana Tomasio
To: gmx-users@gromacs.org
Sent: Wednesday, 9 March 2011 20:07:25
Subject:
If I understand correctly, $2 is the number of hydrogen bonds defined by cutoff
distance and the cutoff angle. $3 is the number of pairs within the cutoff
distance, but beyond the cutoff angle. You may got different number of hbonds
using different cutoff distance and cutoff angle.
Jianguo
__
tion, since there is already one bond formed, then why there is
none pairs in 1000?
On Wed, Mar 16, 2011 at 3:16 PM, Jianguo Li wrote:
If I understand correctly, $2 is the number of hydrogen bonds defined by cutoff
distance and the cutoff angle. $3 is the number of pairs within the cutoff
dist
If you use CHARMM FF and Gromacs4.5 or later, you can use -ter in pdb2gmx and
choose CT2 to add NH2 at C-terminus. For other FF, you may need to manually add
NH2 in pdb file.
Jianguo
From: anna Kalkbrenner
To: gmx-users@gromacs.org
Sent: Sunday, 20 March 2
Dear all,
My molecule contains -CH=CH- fragment and I am trying to create the topology
using Charmm FF. It seems that there is no improper dihedrals for -CH=CH-
fragment in Charmm FF, while other FF (e.g., Amber or OPLS) has additional
improper dihedrals terms for that fragment.
Could anybody
I equilibrated the system for about 20ns at 300K.
Jianguo
From: albert
To: Jianguo Li
Cc: Discussion list for GROMACS users
Sent: Monday, 30 May 2011 14:52:23
Subject: Re:Re: Re: [gmx-users] is it possible to convert NAMD psf file to
gromacas format
Seems gravity is much weaker than the other forces in molecular simulations and
thus can be neglected.
Jianguo
From: mohsen ramezanpour
To: Discussion list for GROMACS users
Sent: Wednesday, 1 June 2011 15:20:09
Subject: [gmx-users] Gravity force in equation
The error message already shows some hints. Try recompile FFTW with -fPIC.
Jianguo
From: Chandan Choudhury
To: gmx-users
Sent: Thursday, 2 June 2011 15:03:03
Subject: [gmx-users] gmx4.5.4 installation help
Hello gmx-users,
I am trying to install gmx-4.5.4
Dear all,
I have made a test calculation of local pressure using version 4.5 for my
membrane simulation using CHARMM FF. When rerun the simulation, mdrun gives the
localpressure data. Howeve, instead of giving an anveraged data of the local
pressure, mdrun gives a separate file for each frame,
Choubey
To: Jianguo Li ; Discussion list for GROMACS users
Sent: Wednesday, 22 June 2011 00:16:43
Subject: Re: [gmx-users] Re: local pressure v4.5 issues
On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li wrote:
Hi Amit,
>
>May I ask you a question?
>In your calculation of local pressur
s.
Btw, did you use CHARMM FF in your simulations and how did you convert the tpr
files from v 4.5 to v 4.0?
Cheers
Jianguo
From: Amit Choubey
To: Jianguo Li ; Discussion list for GROMACS users
Sent: Friday, 1 July 2011 10:32:07
Subject: Re: [gmx-users]
k you very much!
Cheers,
Jianguo
From: Amit Choubey
To: Jianguo Li
Cc: Discussion list for GROMACS users
Sent: Friday, 1 July 2011 11:47:58
Subject: Re: [gmx-users] Re: local pressure v4.5 issues
On Thu, Jun 30, 2011 at 7:57 PM, Jianguo Li wrote:
Hi
You can specify the energygrps in mdp file, grompp a new tpr file and use
-rerun
option of the mdrun to get a new edr file
Cheers
Jianguo
From: "nishap.pa...@utoronto.ca"
To: gmx-users@gromacs.org
Sent: Tuesday, 7 December 2010 02:56:04
Subject: [gmx-user
There is a solution in this mailing list sometime before:
mv md.log to some other folder and copy it back.
Jianguo
From: lina
To: Discussion list for GROMACS users
Sent: Friday, 13 January 2012, 18:51
Subject: Re: [gmx-users] Failed to lock: md.log. No lock
Another possible reason is due to vmd, which numbers the residue from 0.
Residue 143 in gromacs corresponds to residue 142 in vmd.
Cheers,
Jianguo
From: Du Jiangfeng (BIOCH)
To: "gmx-users@gromacs.org"
Sent: Friday, 3 February 2012, 1:16
Subject: [gmx-users
You can look at gromacs tool g_flux and g_count at:
https://github.com/orbeckst/g_count
Jianguo
From: Yao Yao
To: "gmx-users@gromacs.org"
Sent: Wednesday, 15 February 2012, 10:38
Subject: [gmx-users] water channel
Hi Gmxers,
Happy Valentine's Day!
Sor
Probably you can use g_rdf -surf to get the surface based g(r) for water
molecules, since g(r) is the local_density divided by the average_density, then
local_density=g(r)_surf*average_density, which is a function of distance from
the surface.
Jianguo
From
This paper has used united atoms for -CF3 and -CF2:
Hiroaki et al. Enhanced Hydrophobicity of Fluorinated Lipid Bilayer: A
Molecular Dynamics Study. J. Phys. Chem. B 2008, 112, 11305–11309.
Another way is to use ATB to generate the topology, but I am not sure if it can
deal with fluorine atom
One way to get the free energy is to measure the force as a function of
distance and do the integration to get the PMF, as used in the paper:
Ronen Zangi, Morten Hagen, and B. J. Berne. 2007. Effect of Ions on the
Hydrophobic Interaction betweenTwo Plates. J. AM. CHEM. SOC. 2007, 129,
4678-468
Maybe you can try "trjorder" to order the water molecules around your protein
and make a group of those nearest water molecules and output them using trjconv
Jianguo
From: Sanku M
To: Discussion list for GROMACS users
Sent: Tuesday, 28 February 2012, 7:49
Su
You switched on the position restraint in your mdp file, is that the reason?
From: Albert
To: gromacs maillist
Sent: Sunday, 7 April 2013, 2:47
Subject: [gmx-users] fail to pull
Dear:
I am trying to pull my ligand outside of the binding pocket with followin
Hi Chris,
Perhaps you can try PLUMED+GROMACS. In that case, you can define a collective
variable as mindist between the water molecules and the lipid tails. And then
apply wall potential to keep this CV above a certain value.
Jianguo
From: Christopher Neale
Hi Chris,
Just think of another possible way without modifying the code. The task can be
achieved by increasing the LJ repulsion term between the lipid tail atoms and
water molecules, but keeping all other interactions unchanged. To do so, the
free energy code can be used. You can create a st
There are several ways, usually I do like the following:
1. first construct one leaflet. Use "editconf -translate" to construct a small
box containing with 3 POPE 1 POPE
2. Use "genconf -nbox" to replicate the above in x,y dimension to get 64 lipids
3. Use "editconf -rotate -translate" to get th
After inserting the protein, the equilibrium box length in the x and y
dimension should be different, so you need anisotropic pressure coupling during
the 1st step. After equilibrium, the ratio of box length in x,y is fixed, so
you can use semi-isotropic method.
--Jianguo
___
the job, but I expect it may take longer
time to reach equilibrium.
--Jianguo
From: Justin Lemkul
To: Jianguo Li ; Discussion list for GROMACS users
Sent: Friday, 17 August 2012, 9:19
Subject: Re: [gmx-users] Protein-POPC bilayer
On 8/16/12 9:14 PM
I have met similar problem before. The distance calculated by g_dist is
different from that calculated by grommp, especially when the actual
distance between the two groups is very small. As the actual distance
becomes larger, the difference of the distance from the two commands becomes
smalle
I guess is that g_wham takes the distance from tpr file which calculates the
distance using grommp.
It seems that the distances calculated using g_dist and grompp are different,
as discussed in this forum about 10 days ago.
-Jianguo
- Original Message -
From: Raphael Alhadeff
To:
editconf -princ will put the long axis of the protein in x-direction, after
that you may need editconf -rotate 0 90 0 -c to make it in z-direction
-Jianguo
- Original Message -
From: Shima Arasteh
To: Discussion list for GROMACS users
Cc:
Sent: Tuesday, 11 September 2012, 15:18
Su
One situation is the analysis that require velocities, such as calculating
velocity autocorrelation function or lateral pressure.
-Jianguo
From: Ladasky
To: gmx-users@gromacs.org
Sent: Friday, 12 October 2012, 13:25
Subject: [gmx-users] When are .trr files
It seems difficult to use RMSD as the reaction coordinate to do umbrella
sampling simulations. Maybe you can try meta-dynamics in which you can
use RMSD as a collective to get the free energy. It is implemented in a
modified version of gromacs (GROMETA), or you can use PLUMED together
with curr
If you position restraint the receptor or only use several residues at the
binding site, in both cases you limit your sampling to a small part of the
phase space and the PMF may not be accurate, since the receptor may undergo
conformational change upon ligand binding.
Cheers
--Jianguo
- O
If the two end states of a system are fixed, the free energy difference is
independent of the path. I am not sure what caused the problem, but if besides
the protein, water and ions, there are some other molecules in your simulation
box (e.g., membrane or ligand), the states A and B of your prot
One thing you can try in your membrane simulation is to couple the Protein,
Lipid and Water_Ion separately to the thermal bath.
Cheers,
Jianguo
From: Sheeba Jem
To: gmx-users@gromacs.org
Sent: Wednesday, 6 July 2011 07:05:43
Subject: [gmx-users] REMD with 'b
Lateral pressure is a function of z-distance, maybe you can try simulations
using different surface tension, which is the integration of lateral pressure.
Cheers,
Jianguo
From: KONG Xian
To: gmx-users@gromacs.org
Sent: Wednesday, 27 July 2011 10:58:56
Subje
Use grompp of v4.0.7 to generate the tpr files using CHARMM FF and give this
tpr
file to v4.0.2_local_pressure to rerun the simulation.
Jianguo
From: Amit Choubey
To: Jianguo Li
Cc: Discussion list for GROMACS users
Sent: Thursday, 28 July 2011 09:27:04
I have tried CHARMM FF in v4.0.4 and it does not give error, so it seems
dihedral type 9 has already been implemented in v4.0.4.
Jianguo
From: Jianguo Li
To: Amit Choubey
Cc: Discussion list for GROMACS users
Sent: Thursday, 28 July 2011 15:05:19
Subject
Hi, Kong Xian,
It is better to use SHAKE instead of LINCS since LINCS does not directly yield
pairwise forces, as shown in the paper: Erik Lindahl and Olle Edholm. Spatial
and energetic-entropic decomposition of surface tension in lipid
bilayers from molecular dynamics simulations. JOURNAL OF CH
From: KONG Xian
To: ljg...@yahoo.com.sg
Cc: gmx-users@gromacs.org
Sent: Sunday, 21 August 2011 19:20:50
Subject: Re：the mdp parameters for localpressure calculation using
gromacs-4.0.2_localpressure
Thanks for your kindly reply.
I used the LINCS calculate
you may need to use -ignh option in pdb2gmx.
Jianguo
From: Kamesh Narasimhan
To: "gmx-users@gromacs.org"
Sent: Wednesday, 24 August 2011 14:42:28
Subject: [gmx-users] error:You might need to add atom H to the hydrogen
database
of residue
Hi all,
I a
error.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Jianguo Li [ljg...@yahoo.com.sg]
Sent: Wednesday, August 24, 2011 3:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] error:You might need to add atom H t
Hi,
The .str file contains the information of atomtype, bonds and improper
dihedrals, so it is eneough to write a .rtp file. Then using pdb2gmx to
generate
the itp file.
And you also need to add the missing parameters from CgenFF into the itp
parameter files based on chapter 5, as Justin sug
Why not use CHARMM36 FF? It is available in gromacs user contribution website.
If I remember correctly, charmm27 cannot yield correct area/lipid, you need to
apply surface tension.
Cheeers,
Jianguo
From: Jackson Chief
To: gmx-users@gromacs.org
Sent: Monday, 5
You can either use -ighn option in pdb2gmx or mannualy rename the atom names in
the pdb file.
Cheers,
Jianguo
From: KONG Xian
To: gmx-users@gromacs.org
Sent: Tuesday, 13 September 2011 15:36:41
Subject: [gmx-users] how to handle different atom names between
The first residue number in VMD is 0, not 1.
Jianguo
From: aiswarya pawar
To: Discussion list for GROMACS users
Sent: Friday, 16 September 2011 1:21 PM
Subject: [gmx-users] residue numbering different
Hi Users,
When i list the residues in a index file it show
I met the similar problem before, sometimes my job writes output, sometimes
not. My cluster administrator fixed the problem and they told me that there
were some problem at some compute nodes which my job unfortunately was
dispatched to.
Jianguo
From: lina
which gromacs version are you using? cMAP is implemented in v4.5 or later
Jianguo
From: César Ávila
To: Discussion list for GROMACS users
Sent: Sunday, 9 October 2011 12:07 AM
Subject: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff
I would like to ru
dipeptide in Charmm27 ff
To: "Jianguo Li" , "Discussion list for GROMACS users"
Date: Monday, 10 October, 2011, 5:51 PM
v4.5.4
As I commented above, I had to manually add an entrance for the cmap terms in
the topology file as pdb2gmx would not generate them for the alanine dipept
Dear All,
Has anyone has Gromacs benchmark on Bluegene/Q?
I recently installed gromacs-461 on BG/Q using the following command:
cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \
-DGMX_BUILD_OWN_FFTW=ON \
-DBUILD_SHARED_LIBS=OFF \
-DGMX_XML=OFF \
-DCMAKE
Job queue ( default is normal )
srun --ntasks-per-node=32 --overcommit
/scratch/home/biilijg/package/gromacs-461/bin/mdrun -s box_md1.tpr -c
box_md1.gro -x box_md1.xtc -g md1.log >& job_md1
Cheers
Jianguo
- Original Message -----
From: XAvier Periole
To: Jianguo Li ; Discussi
e a optimized number for --ntasks-per-node?
Cheers
Jianguo
From: Mark Abraham
To: Discussion list for GROMACS users
Cc: Jianguo Li
Sent: Tuesday, 4 June 2013, 22:32
Subject: Re: [gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q
On Tue, Jun 4, 2
You can try move "md.log" to some folder and then copy back such as:
1) mv md.log /some_folder
2) cp /some_folder/md.log .
It works for me
Jianguo
- Original Message -
From: zhaowh
To: gmx-users ; gmx-users ;
gmx-users ; gmx-users ; gmx-users
; gmx-users
Cc:
Sent: Friday, 1
Dear All,
I am working on the interaction of a positively charged peptide (18AA) and the
bacterial membrane consisting of a mixture of zitterionic and negatively
charged lipids. Our experiments show that the peptide can disrutp the membrane.
One problem puzzed me is that which method to use i
Dear all,
I was trying to add two walls at z=0 and z=z_box to my system which contains
one
peptide and one membrane. Since I am interested in how the peptides affect
membrane properties (i.e., area per lipid), I need to use semi-isotropic
pressure coupling. But I wanted to mimick the two-dimen
Hi All,
I found there is a customised version "gromacs-4.0.2_localpressure" for
calculating the local pressure from the Gromacs website. I am wondering is
there
a higher version? The reason is that I am using CHARMM FF and have done
membrane simulations using Gromacs-4.5. If I understand cor
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