- Original Message -
From: fang yuan
Date: Tuesday, August 24, 2010 4:52
Subject: Re: [gmx-users] Does anyone know how to get the file
charmm_gromacs.tar.gz?
To: Discussion list for GROMACS users
> Hi, I have the same problem, I need to implement the general CHARMM
> forcefield in gr
Olá,
Mark and Justin.
Solved.
I did what you suggested and I got all the default values.
Muito obrigado!
eef
___
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 092
On Mon, August 23, 2010 12:12 PM, Eudes Fileti wrote:
> Well, the line 40 is just one of the 36 parameters not found!
> In this link ( https://sites.google.com/site/fileti/ ) I put
> the complete files.
> I know I need to determine which bond type should be called
> and I believe that it has bee
Also, again, as David said, if you find any errors in the parameters or in the
code, please let me know!
Cheers
/Per
23 aug 2010 kl. 20:09 skrev Per Larsson :
> Hi!
>
> Values in columns 1-3 are not currently used in version beta3. They pertain
> to more elaborate surface area algorithms, th
Hi, I have the same problem, I need to implement the general CHARMM
forcefield in gromacs, so I need to know how to convert the rtf files into
rtp files in gromacs
On Sun, Aug 22, 2010 at 10:11 AM, David van der Spoel
wrote:
> On 2010-08-22 15.16, Michael McGovern wrote:
>
>> I'm looking for an r
tekle...@ualberta.ca wrote:
Dear Justine,
I got it and works fine.
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.7047197 -0.3054392 -0.15599120.6156325
19002.0000.7591453 -0.2601027 -0.26593630.6617599
19004.000
Dear Justine,
I got it and works fine.
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
19000.0000.7047197 -0.3054392 -0.15599120.6156325
19002.0000.7591453 -0.2601027 -0.26593630.6617599
19004.0000.7763510 -0.3043177 -0
Hi!
Values in columns 1-3 are not currently used in version beta3. They pertain to
more elaborate surface area algorithms, the one from Still et al in particular.
Column 4 is the Vdw-radii for atom types that are used for computing the Born
radii. The dielectric offset is specified in the mdp-f
On 2010-08-23 19.27, Elizabeth Ploetz wrote:
Dear Gromacs Users,
I am interested in implementing implicit solvent using the OBC GBSA method. In
the Gromacs 4.5beta3 top directory, several force fields (oplsaa and multiple
versions of amber) contain the gbsa.itp file, and one (charmm27), conta
tekle...@ualberta.ca wrote:
Dear Justine,
Reading file PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr, VERSION 3.3.3 (single
precision)
Group 0 ( System) has 28708 elements
Group 1 ( PAP) has 512 elements
Group 2 ( HEP) has 28196 elements
Group 3 (RING) has
Dear Justine,
Reading file PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr, VERSION 3.3.3
(single precision)
Group 0 ( System) has 28708 elements
Group 1 ( PAP) has 512 elements
Group 2 ( HEP) has 28196 elements
Group 3 (RING) has20 elements
Select a group
Dear Gromacs Users,
I am interested in implementing implicit solvent using the OBC GBSA method. In
the Gromacs 4.5beta3 top directory, several force fields (oplsaa and multiple
versions of amber) contain the gbsa.itp file, and one (charmm27), contains a
gb.itp file. They all have the same co
- Original Message -
From: Eudes Fileti
Date: Tuesday, August 24, 2010 3:22
Subject: Re: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Mark]
To: gmx-users@gromacs.org
> Hello Mark thanks for the comments,
> In fact, what I did was insert the parameters into ffbonded.itp fi
tekle...@ualberta.ca wrote:
The following is the out put.
# This file was created Mon Aug 23 11:18:45 2010
# by the following command:
# /home/software/gromacs/3.3.3/bin/g_dist -f
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2 -o
Di
The following is the out put.
# This file was created Mon Aug 23 11:18:45 2010
# by the following command:
# /home/software/gromacs/3.3.3/bin/g_dist -f
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.xtc -s
PAP_8_Box12_HEP_EM_NPTNHPR_20ns.tpr -n index.ndx -b 19000 -e 2 -o
DistPAP8HEP.xvg
#
# /home/sof
Dear Gromacs users,
I run my simulation for 20ns and want to extract aromatic-aromatic
distance to see the stacking issue. But I am unable to get the value.
I have 24 molecules in my simulation and filled with solvents.
My index file is like that:
[ System ]
123456
Hello Mark thanks for the comments,
In fact, what I did was insert the parameters into ffbonded.itp file.
What I presented the link above is just the part that I had added
(of course there is the line 1495, not shown!).
The installation where I started making the change is new,
I have not changed
Hi there,
I have a system with 'HISE' and using gmx 4.5.
ATOM 20 N HISE2 6.376 3.718 -0.053 1.00 0.00
N
ATOM 21 H HISE2 5.980 4.646 -0.135 1.00 0.00
H
ATOM 22 CA HISE2 7.843 3.744 -0.109 1.00 0.00
C
ATOM 23 HA HISE2
- Original Message -
From: Eudes Fileti
Date: Tuesday, August 24, 2010 2:12
Subject: Re: Re: [gmx-users] Charmm to Gromacs: Polyols force field [Justin]
To: gmx-users@gromacs.org
> Hello Justin, thanks again.> Well, the line 40 is just one of the 36
> parameters not found!> In this lin
Hello Justin, thanks again.
Well, the line 40 is just one of the 36 parameters not found!
In this link ( https://sites.google.com/site/fileti/ ) I put the complete
files.
I know I need to determine which bond type should be called and I believe
that it has been done, but I don't know why it's not b
Hi,
you don't write what network you have and how many cores per node. If it is
ethernet it will be difficult to scale.
You might want to try the 4.5beta version because we have improved the
scaling with it. Also there is a tool g_tune_pme which might help you.
Roland
On Mon, Aug 23, 2010 at 11:
Hi,
I have been playing with the "mdrun_mpi" command in gromacs 4.0.7 to try out
parallel processing. Unfortunately, the results I got did not show any
significant improvement in simulation time.
Below is the command I issued:
mpirun -np x mdrun_mpi -deffnm
where x is the number of proc
pawan raghav wrote:
Below is the hbond.xvg content 1 coloumn is for time second for numbers,
but I am not getting for 3rd one i.e. Pairs within 0.35 nm is this shows
area in cutoff range?
Search the mailing list archive. I answered this identical question last week.
If you use the phr
trying to calculate pmf for enzyme ligand complex using the tutorial
> of umbrella sampling.
> I have successfully created the unit cell around the protein and have
> solvated. The ions were also added by genion.
> But when I run the minimization step with the command
> grompp -f minim.mdp -c solv
Below is the hbond.xvg content 1 coloumn is for time second for numbers,
but I am not getting for 3rd one i.e. Pairs within 0.35 nm is this shows
area in cutoff range?
@ title "Hydrogen Bonds"
@ xaxis label "Time"
@ yaxis label "Number"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ l
anks in advace
Many regards
Abdul Wadood,
Research Scholar,
Dr.Panjwani Center for Molecular Medicine and
Drug Research,
International Center for Chemical and
Biological Science,
University of Karachi, Karachi-75720, Pakistan.
Email:wadoodbiochem...@hotmail.com
<mailto
abdul wadood wrote:
Hi, All
I am trying to calculate pmf for enzyme ligand complex using the
tutorial of umbrella sampling.
I have successfully created the unit cell around the protein and have
solvated. The ions were also added by genion.
But when I run the minimization step with the comma
As David said, the reading/writing is done in src/gmxlib/enxio.c, but you could
also read edr files indirectly through gmxdump: that should also give you an
idea of the type of information in those files.
On Aug 22, 2010, at 13:14 , Alan Wilter Sousa da Silva wrote:
> Hi there,
>
> I am tryi
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