I think your original problem is that you define only one charge group for the
entire molecule/polymer. You need to define each bead in a separate charge
group and things will be fine :)) you do not have charges anyways.
As far as I know angles have never made martini unstable but the conventi
I am a new user of Gromacs, I have problem with genbox. When I run genbox
following error occurred:Program genbox, VERSION 4.5.5Source code file:
/build/buildd/gromacs-4.5.5/src/gmxlib/futil.c, line: 491File input/output
error:/home/mijiddorj/Desktop/Tutorial02/1AKI1.topFor more information and
tip
Justin,
I've already tried use g_x2top for the model of the system built from
regularly spaced C-atoms ( with included hydrogens to specify sp3
hybridization).
By means of that command I've created topology for my lattice with big
force constant ( for the simulation of the very rigid structure)
On 1/2/13 4:36 AM, James Starlight wrote:
Justin,
I've already tried use g_x2top for the model of the system built from
regularly spaced C-atoms ( with included hydrogens to specify sp3
hybridization).
By means of that command I've created topology for my lattice with big
force constant ( fo
On 1/2/13 4:20 AM, Mijiddorj wrote:
I am a new user of Gromacs, I have problem with genbox. When I run genbox
following error occurred:Program genbox, VERSION 4.5.5Source code file:
/build/buildd/gromacs-4.5.5/src/gmxlib/futil.c, line: 491File input/output
error:/home/mijiddorj/Desktop/Tutorial
Justin,
so why my simulation of the sp3 lattice have been crashed with the
links warnings ( which always tells about wrong geometry in topology)?
also I've tried to paraetrize completely planar (sp2) lattice but
obtain errors like that
Can not find forcefield for atom C27-22 with 2 bonds
Can not
On 1/2/13 7:03 AM, Turgay Cakmak wrote:
Dear gromacs users,
I am trying to solvate several peptides (at a desired positions) in a
dodecahedron box. I have done following steps;
1) editconf -f peptides.gro -o peptides_nb.gro -c -d 1.0 -bt dodecahedron
2) genbox -cp peptides_nb.gro
On 1/2/13 7:15 AM, James Starlight wrote:
Justin,
so why my simulation of the sp3 lattice have been crashed with the
links warnings ( which always tells about wrong geometry in topology)?
Incorrect geometry is not the only cause of LINCS warnings. I haven't seen
nearly enough information
On Wed, Jan 2, 2013 at 1:15 PM, James Starlight wrote:
> so why my simulation of the sp3 lattice have been crashed with the
> links warnings ( which always tells about wrong geometry in topology)?
I might have missed something from the beginning of this discussion...
Why do you use LINCS with a l
Bogdan,
Thank you for explanation. Indeed the problem was in the LINCS
constrains which was not required for the lattice system.
By the way now I'd like to simulate the same 2D flexible ( in non
planar hybridization) lattice but consist of non-hydrogens atoms only
( only atoms forming lattice sca
by the way also I'd like to know what options for the pbc should I
specify that my system looked like infinite lattice in the x-y dims ?
James
2013/1/2, James Starlight :
> Bogdan,
>
> Thank you for explanation. Indeed the problem was in the LINCS
> constrains which was not required for the latti
Thank you, I got it.
Mijiddorj
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Hello all, I am new user of gromacs. I am doing Tutorial 1. When I run
grompp, following problem occurred:Program grompp, VERSION 4.5.3Source code
file: toppush.c, line: 1987Fatal error:No such moleculetype CL-For more
information and tips for troubleshooting, please check the GROMACSwebsite at
htt
On 1/2/13 10:01 AM, Mijiddorj wrote:
Hello all, I am new user of gromacs. I am doing Tutorial 1. When I run
grompp, following problem occurred:Program grompp, VERSION 4.5.3Source code
file: toppush.c, line: 1987Fatal error:No such moleculetype CL-For more
information and tips for troubleshootin
On 1/2/13 8:58 AM, James Starlight wrote:
Bogdan,
Thank you for explanation. Indeed the problem was in the LINCS
constrains which was not required for the lattice system.
By the way now I'd like to simulate the same 2D flexible ( in non
planar hybridization) lattice but consist of non-hydroge
On 1/2/13 9:26 AM, James Starlight wrote:
by the way also I'd like to know what options for the pbc should I
specify that my system looked like infinite lattice in the x-y dims ?
Do you want the lattice to be infinite or do you just want it to look like it's
infinite? If you want an infini
On Wed, Jan 2, 2013 at 2:58 PM, James Starlight wrote:
> By the way now I'd like to simulate the same 2D flexible ( in non
> planar hybridization) lattice but consist of non-hydrogens atoms only
> ( only atoms forming lattice scaffold ). Does it possible to change
> Carbon atom-valence (from 4 to
On 1/2/13 10:14 AM, Bogdan Costescu wrote:
On Wed, Jan 2, 2013 at 2:58 PM, James Starlight wrote:
By the way now I'd like to simulate the same 2D flexible ( in non
planar hybridization) lattice but consist of non-hydrogens atoms only
( only atoms forming lattice scaffold ). Does it possible t
Dear Justin, Thank you for your helpful suggestion.
Mijiddorj
From: Justin Lemkul [via GROMACS]
To: Mijiddorj
Sent: Wednesday, January 2, 2013 11:10 PM
Subject: Re: grompp error
On 1/2/13 10:01 AM, Mijiddorj wrote:
> Hello all, I am new user of groma
Hi, all.
Does anybody know wether I have to put a phosphorylated residue in the
kinase's activation loop (last example is pdbid 2Y94) or not, when I'm
working with protein-inhibitor complex without any type of
protein-protein interactions? Or it is necessary only when I'm working
with p-p complexes
Hi,
In order to make an amidated c-terminal, I used CT2 in charmm ff at the
c-terminal. The last residue of my peptide is serine, and the total charge of
peptide is should to be +5.00 . After running pdb2gmx, choosing CT2 at the
c-terminal, and then getting top file, when I see the top file,
On 1/2/13 2:07 PM, Shima Arasteh wrote:
Hi,
In order to make an amidated c-terminal, I used CT2 in charmm ff at the
c-terminal. The last residue of my peptide is serine, and the total charge of
peptide is should to be +5.00 . After running pdb2gmx, choosing CT2 at the
c-terminal, and th
Justin,
I want to simulate flexible lattice consist of only one type of atoms
(nodes). So the planar (sp2 ) carbons are rigid. On other hand more
flexible (sp3) carbons connected with hydrogens but I want that
hydrogens were not included in my lattice. Should I use another
(what? )atom-type for t
Dear gromac users,
after running a successful NVT, I was going to run NPT. (All ran with MPI),
however when I attempt to run the NPT, I get the following segmentation error:
Getting Loaded...
Reading file npt.tpr, VERSION 4.5.3 (single precision)
Loaded with Money
WARNING: This run will gener
Dear gromac users,
after examining my nvt run outcome, I see that my molecule has half of the arm
stuck outside of the box (I guess my run wasn't very successful). But I thought
the jumping outside of the box would be corrected by periodic boundary? Should
I run my nvt for longer since the stru
On 1/2/13 3:08 PM, James Starlight wrote:
Justin,
I want to simulate flexible lattice consist of only one type of atoms
(nodes). So the planar (sp2 ) carbons are rigid. On other hand more
flexible (sp3) carbons connected with hydrogens but I want that
hydrogens were not included in my lattice
On 1/2/13 3:20 PM, Xu Dong Huang wrote:
Dear gromac users,
after examining my nvt run outcome, I see that my molecule has half of the arm
stuck outside of the box (I guess my run wasn't very successful). But I thought
the jumping outside of the box would be corrected by periodic boundary? Sh
@Justin, here are the details of my NVT and NPT .mdp, (All ran without position
restraint) , + details of the NVT run
For NVT.mdp:
integrator = md
tinit= 0.0
dt = 0.02
nsteps = 1
nstcomm = 1
comm-grps
@Justin,
forgot to mention, yes the NVT was ran using MPI as well. (You're right, the
MPI is not the issue, because I took the file off my cluster and attempted to
run NPT on my personal computer, it reported same segmentation error, fault 11)
Xu Dong Huang
Chemical & Biochemical Engineering
Ru
On 1/2/13 3:42 PM, Xu Dong Huang wrote:
@Justin, here are the details of my NVT and NPT .mdp, (All ran without position
restraint) , + details of the NVT run
For NVT.mdp:
integrator = md
tinit= 0.0
dt = 0.02
nsteps = 10
Dear Justin,
I will try your suggestion to rerun it on Berendsen coupling and see if there
is any further problems. The system indeed contain the star shaped structure I
showed you earlier (running multiple versions, containing from 1, 5, 10, 15 and
20 stars in a solvent box), the solvent is ju
The version of GROMACS I'm using is 4.5.5.
I checked the aminiacids.rtp file in charmm36 folder, I see + 0.51 for carbonyl
C. Is there any problem with the C36 which I use?
[ SER ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09
The version of GROMACS I'm using is 4.5.5.
I checked the aminiacids.rtp file in charmm36 folder, I see + 0.51 for carbonyl
C. Is there any problem with the C36 which I use?
[ SER ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.0
Justin,
I want to simulate lattice with flexible nodes ( to examine
fluctuations of that system by mens of Normal Mode Analysis). If I
choose sp3 carbons as the nodes I obtain such lattice. But In that
system hydrogens are also present which are not desirable in my system
( i want system consiste
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