Dear Sir,
When I run g_rms -s md.tpr -f md.trr -o rmsd.xvg, the program requires me
selecting a group twice as following:
g_rms -s md.tpr -f md.trr -o rmsd.xvg后, 程序两次要求选结构组,如下:
Reading file md.tpr, VERSION 3.3.1 (single precision)
Reading file md.tpr, VERSION 3.3.1 (single precision)
Select
You could start by reading the gromacs manual,
Section 8.9
On 12/20/11 9:30 AM, yp sun wrote:
Dear Sir,
When I run g_rms -s md.tpr -f md.trr -o rmsd.xvg, the program requires
me selecting a group twice as following:
g_rms -s md.tpr -f md.trr -o rmsd.xvg?, ??? ? ??,??:
Reading file md.tpr, V
Dear GMX-users
I am working on lipid-drug system.I have done these stages:
1.creating topology for drug and lipid
2.solvation
3.Ion addition
4.Energy minimization
5.NVT
My question is,why does the energy and temperature curves converge to
zero(I have used 320 K for my temperature in mdp file)?
Tha
hello sir,
i go through the manual and your link..
i need to add BFC residue type in rtp file and residuetype.dat..
thing is i need to include charges angles bonds dihedrals impropers for
residue in my rtp file ,,
i dono how to define its value..
mine is 14 carbon fattyacid..(BFC)
give some idea
Dear GROMACS users,
I have done Normal Mode Analysis and have calculated partial charges and
the optimized geometry of a few compounds using high-level QM calculations.
Now I want to see (if possible) how well GROMACS can reproduce the normal
modes if I start from the same optimized geometry and
Hi Devs,
Is this intended or just a typo:
#nb_kernel_x86_64_sse/nb_kernel_x86_64_sse.c#
.:
211:fprintf(log,"Testing x86_64 SSE2 support...");
.:
##
instead of:
.:
211:fprintf(log,"Testing x86_64 SSE1 support...");
.:
The same thing appears in other "_sse.c" files.
Thanks,
Da
On 20/12/11, priya thiyagarajan wrote:
> hello sir,
> i go through the manual and your link..
> i need to add BFC residue type in rtp file and residuetype.dat..
> thing is i need to include charges angles bonds dihedrals impropers for
> residue in my rtp file ,,
>
> i dono how to define it
On 20/12/11, Thomas Evangelidis wrote:
> Dear GROMACS users,
>
>
> I have done Normal Mode Analysis and have calculated partial charges and the
> optimized geometry of a few compounds using high-level QM calculations. Now I
> want to see (if possible) how well GROMACS can reproduce the norm
On 20/12/11, parto haghighi wrote:
> Dear GMX-users
> I am working on lipid-drug system.I have done these stages:
> 1.creating topology for drug and lipid
> 2.solvation
> 3.Ion addition
> 4.Energy minimization
> 5.NVT
> My question is,why does the energy and temperature curves converge to
> zer
i went through the mailing list, but i dont understand when i run the same
protein on my computer it runs correctly without any LINCS warning. On the
cluster with 64 processors the job runs but crashes in between and shows
the LINCS warning.
Please anyone tell me what could be the reason. Is anyt
On 20/12/11, aiswarya pawar wrote:
> i went through the mailing list, but i dont understand when i run the same
> protein on my computer it runs correctly without any LINCS warning. On the
> cluster with 64 processors the job runs but crashes in between and shows the
> LINCS warning.
>
T
Mark, thanks for the prompt response!
I have done Normal Mode Analysis and have calculated partial charges and
> the optimized geometry of a few compounds using high-level QM calculations.
> Now I want to see (if possible) how well GROMACS can reproduce the normal
> modes if I start from the same
Dear Users,
I am trying to reproduce the results obtained by Fox & Kollman on
chloroform presented in the following papers but can never achieve the
proper density of 1.459 they obtain with their own rigid CHCL3 model.
The best I obtain with the parameters presented below is 1.390. I
trie
On 2011-12-20 15:03, ana...@fundp.ac.be wrote:
Dear Users,
I am trying to reproduce the results obtained by Fox & Kollman on
chloroform presented in the following papers but can never achieve the
proper density of 1.459 they obtain with their own rigid CHCL3 model.
The best I obtain with the par
--- Begin Message ---
Hi
I want to run an NPT simulation with all h-bonds constrained. How does
grompp identify the Hydrogen atoms given that forcefield labels like HA,
HC, HE are used. Is it the mass?
Many Thanks
Gavin
--- End Message ---
--
gmx-users mailing listgmx-users@gromacs.org
ht
Dear justin , i regret inconvenience in the previous mail
Instead of taking PDB based on g_dist over all frames Can i choose various
.gro files for doing umbrella sampling based on the pullf.xvg . file
In that file plot of force Vs time is available. i am selecting the PDBs from
near ma
Hi,
I have a technical question regarding feasibility of combining replica
exchange with umbrella sampling or any other pulling simulations in gromacs.
Since the umbrella sampling or any other pulling simulations are
non-equilibrium simulation due to presence of external bias, I wonder whether
Gavin Melaugh wrote:
Subject:
h-bonds constraints
From:
Gavin Melaugh
Date:
Mon, 19 Dec 2011 10:20:40 +
To:
Discussion list for GROMACS users
To:
Discussion list for GROMACS users
Hi
I want to run an NPT simul
vidhya sankar wrote:
Dear justin , i regret inconvenience in the previous mail
I have no experience with PLUMED; I could not comment. I have been extremely
busy lately.
Instead of taking PDB based on g_dist over all frames Can i choose
various .gro files for doing umbrella sampling ba
Dear gmx-users,
I've just finished several simulations of 4 single point mutants of my
dimeric protein in rhombic dodecahedron box (-d 1.5 nm) centered on the
protein, filled with water, neutralized with sodium, simulated with Gromacs
4.5.3 for 30 ns after NVT and NPT dynamics. I made simulations i
Hi Anna,
Jumps like that are a consequence of PBC. Nothing wrong. Removing jumps
like you did is the proper treatment.
Cheers,
Tsjerk
On Dec 20, 2011 9:27 PM, "Anna Marabotti" wrote:
**
Dear gmx-users,
I've just finished several simulations of 4 single point mutants of my
dimeric protein in r
Hi,
I am simulating DOPC lipid molecules in water, i would like to plot the
pressure profiles, for the systems i have . Can someone tell me , is there any
option in GROMACS which can give the pressure profile?
Ramya Parthasarathi
ramya.sar...@aol.com
--
gmx-users mailing listgmx-users@g
Thanks a lot , will try that
Ramya Parthasarathi
ramya.sar...@aol.com
-Original Message-
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Fri, Dec 16, 2011 11:16 am
Subject: Re: [gmx-users] Voronoi tessellation
Ramya Parthasarathi wrote:
> Hi
>
> I am working
It will be saved in the .edr file. Use g_energy to extract the data you are
interested in.
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
On 12/21/2011 12:57 AM, Thomas Evangelidis wrote:
Mark, thanks for the prompt response!
I have done Normal Mode Analysis and have calculated partial
charges and the optimized geometry of a few compounds using
high-level QM calculations. Now I want to see (if possible) how
well G
Dear all,
I prepare to do simulation about the solution of CTAB. Does anyone know the
force field (top and gro files) of CTAB which were published before?
Thank you very much.
Best regards,
Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981
--
gmx-users ma
Hi,
this is on purpose. Since 4.5 GROMACS requires SSE2. It is used for e.g.
the GB kernels. Because CPUs with SSE1 support but no SSE2 are so old we
don't try to support them anymore even for those kernels not requiring SSE2.
Roland
On Tue, Dec 20, 2011 at 6:05 AM, Daniel Adriano Silva M
wrote:
On 12/19/2011 1:51 PM, Ben Reynwar wrote:
I'm having a problem with gromacs not terminating as expected when
using the maxh option.
It is an REMD simulation with 32 replicas.
I'm specifying -maxh 24 and as expected see the following in the stderr output.
Step 773882: Run time exceeded 23.760 hou
Got it. Thanks.
Daniel
On Dec 21, 2011 9:46 AM, "Roland Schulz" wrote:
> Hi,
>
> this is on purpose. Since 4.5 GROMACS requires SSE2. It is used for e.g.
> the GB kernels. Because CPUs with SSE1 support but no SSE2 are so old we
> don't try to support them anymore even for those kernels not requ
hello sir,
Thanks for your reply..
As you suggest i tried with all available forcefield for my lipopeptide but
i am getting the same error,,
*Processing chain 2 'A' (16 atoms, 1 residues)
Warning: Starting residue BFC1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or
priya thiyagarajan wrote:
hello sir,
Thanks for your reply..
As you suggest i tried with all available forcefield for my lipopeptide
but i am getting the same error,,
I have posted this link several times before:
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Fi
As suggested by David I extended the simulations (total of 25ns) for a
single chain polyacid in 5500 water molecules and tried to calculate the
H-bond ACF. I get the same negative lifetime for Hbonds between COOH groups
and water. Is it that the g_hbond ACF giving weird results for this case.
For c
Hi,
I am running MD simulation for my system using Gromacs , as the output
energies values generated are in the units of kJ/mol , Is there any option
or method while running the simulation which i can use so that i get
output energies in the units of kcal/mol rather than in kJ/mol.I have gone
thr
On 12/21/2011 5:44 PM, Sairam Tatikonda wrote:
Hi,
I am running MD simulation for my system using Gromacs , as the
output energies values generated are in the units of kJ/mol , Is there
any option or method while running the simulation which i can use so
that i get output energies in the uni
hello sir,
thanks for your reply..
sorry for disturbing you again and again..
i understood that i need to add my residue BFC in my rtp file and
residuetype.dat file.
i like to clarify one thing.
i added BFC as lipid in my residuetypes.dat file.
then i need to include my residue BFC in .rtp file.
T
On 12/21/2011 5:53 PM, priya thiyagarajan wrote:
hello sir,
thanks for your reply..
sorry for disturbing you again and again..
i understood that i need to add my residue BFC in my rtp file and
residuetype.dat file.
i like to clarify one thing.
i added BFC as lipid in my residuetypes.dat file.
t
Dear Everyone:
I need to calculate the free energy change of restraining the ligand in the
binding site. I wonder if or not the restraint force can be directly controlled
by the free energy code, which means by different lambda values. I checked the
manual of gromacs 4.5.4 but can not found
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