kitty ji wrote:
> Dear GMX user,
>
>
>
> Explicated model of Poly (vinyl methyl ether) was built with ether
> parameters in OPLS Force Field. The density and radius of gyration of
> PVME melts fit experimental value well. And then it was solvated in Tip5p.
>
>
>
> In experiment, PVME shou
Hi George,
And what does the .log tell you? Did grompp give any errors? Did
energy minimization succeed?
Cheers,
Tsjerk
On 4/24/07, George Abadir <[EMAIL PROTECTED]> wrote:
It says:
"Starting mdrun 'ICE in water'
30 steps, 45.0 ps
Back off! I just backed up final traj.trr to ./#finaltra
Hi Luciano,
Look in the topology file where your metal complex is defined (under
each [ ] section, but this seems to me to be a dihedral). You've not
given enough parameters for one of the bonded definitions.
Furthermore, it is likely that the error is in the .rtp entry,
assuming you generated on
Dear GMX user,
Explicated model of Poly (vinyl methyl ether) was built with ether parameters
in OPLS Force Field. The density and radius of gyration of PVME melts fit
experimental value well. And then it was solvated in Tip5p.
In experiment, PVME should solvate in water well in ~300k. How
It says:
"Starting mdrun 'ICE in water'
30 steps, 45.0 ps
Back off! I just backed up final traj.trr to ./#finaltraj.trr.20#
Segmentation Fault"
Thank you,
George
Mark Abraham wrote:
George Abadir wrote:
Hi,
I am doing a simulation of a carbon nanotube in water. I have
done the ene
George Abadir wrote:
Hi,
I am doing a simulation of a carbon nanotube in water. I have done
the energy minimization successfully and when I passed to the molecular
dynamics simulation it terminated with "Segmentation Fault". It seems
the only way to bypass this is to reduce the time step "
Hi,
I am doing a simulation of a carbon nanotube in water. I have done
the energy minimization successfully and when I passed to the molecular
dynamics simulation it terminated with "Segmentation Fault". It seems
the only way to bypass this is to reduce the time step "dt" to 0.1 fs
which i
Hi Everybody,
I have been working with the topolgy file creating a new residue type to
include some metal-aminoacids ligand complex.
So far, pdb2gmx provide the topology file without errors and this file seems to
contain all te interaction I added in the correspondign databases. However, the
g
Arthur Roberts wrote:
Hi, all,
I need to be able to execute commands by a script and
I need the commands to be non-interactive.
One example of the commands that I use is g_rms.
echo 3 3 | g_rms flags
How can I make this command totally non-interactive?
Thank you in advance,
Best wishes,
Hi, all,
I need to be able to execute commands by a script and
I need the commands to be non-interactive.
One example of the commands that I use is g_rms.
How can I make this command totally non-interactive?
Thank you in advance,
Best wishes,
Art Roberts
University of Washington
Department of
Hi Stan,
I suggest you may find solution outside Gromacs. Use Pymol or other
software to simply add hydrogen. Check it (usually they will ignore some
double bonds) and put it back to GROMACS.
This is not encouraged and likely would not solve your problems (sorry
Yang Ye).
The .hdb format does
I suggest you may find solution outside Gromacs. Use Pymol or other
software to simply add hydrogen. Check it (usually they will ignore some
double bonds) and put it back to GROMACS.
Regards,
Yang Ye
On 4/23/2007 5:24 PM, Stas Bobritsky wrote:
Hi all!
I`m working on tRNA MD. My structure con
Hi,
Use make_ndx you will see the default grouping of atoms. Type 'q' to
quit and save the index.ndx.
Those 149 atoms shall be from residue name that is unknown to Gromacs,
find it from their index number from index.ndx and add to aminoacid.dat
(increment the number on top as well) located at top
When posting questions you need to give more information. "I prepared
dopc.itp parameter file for DOPC lipid bilayer." -- last thing I heard
you were talking about two very different parameter sets, so I get
confused. If you are going with the Berger parameters then for arbitrary
protein ff com
Daniel Rigden wrote:
Dear all
I'm trying to compile the latest GROMACS 3.3.1 on the latest Ubuntu
Linux. Due to some fftw installation issue I used
./configure --with-fft=fftpack
make
make install
All seemed to work fine, but any program I try to run now gives me a
crash of this kind
[EMAI
Hi,
Unfortunately that's exactly the one :-)
You can search the mailing list online for details, but there's a
post from 20070323 where Chris Neale reported success after
downgrading to cc (GCC) 3.3.6 (Ubuntu 1:3.3.6-13ubuntu2). No
guarantees though, since he didn't seem to have exactly th
Hi Erik
Thanks for the reply. Yes, I get this
cc (GCC) 4.1.2 20060928 (prerelease) (Ubuntu 4.1.1-13ubuntu5)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is
NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICU
Hi Daniel,
Could you run
cc --version
and post the result? Apparently some new Linux distributions are
shipping with a buggy prerelease of gcc.
Cheers,
Erik
On Apr 23, 2007, at 5:21 PM, Daniel Rigden wrote:
Dear all
I'm trying to compile the latest GROMACS 3.3.1 on the latest Ubuntu
L
Hi everyone
I'd like to convert my Gromacs trajectory to an Amber format for use
with the CAVER program. Reading round, it seems that Amber is
equivalent to the g87 format so I can use trjconv to produce the file.
This all seems to work well (the file gets read in and processed) except
for a prob
Dear all
I'm trying to compile the latest GROMACS 3.3.1 on the latest Ubuntu
Linux. Due to some fftw installation issue I used
./configure --with-fft=fftpack
make
make install
All seemed to work fine, but any program I try to run now gives me a
crash of this kind
[EMAIL PROTECTED]: g_clustsiz
But in the [molecules] entry of my top file, there are only "Protein SOL
Cl"
I don't know why the 149 atoms are not included.
How I check them?
Thanks in advance!
ÔÚÄúµÄÀ´ÐÅÖÐÔø¾Ìáµ½:
>From: Mark Abraham <[EMAIL PROTECTED]>
>Reply-To: Discussion list for GROMACS users
>To: Discussion li
Hi everybody
Thank you very much Tsjerk. I'm sorry for asking all these questions
but some points are still unclear to me, and I didn't find much
information on the mailing list archives or in the manual that could
help me.
Grompp is complaining about the angles because in the .top file ther
naga raju wrote:
Dear gmx users,
I am thankful to Tsjerk Wassenaar and Chris
Neale, to their suggestions. I prepared dopc.itp parameter file for DOPC
lipid bilayer. To Protein+DOPC bilayer system, which force field I have
to choose to my protein.
You need to put th
Stas Bobritsky wrote:
After pdb2gmx -f trna.pdb -o trna.gro -v Gromacs says:
WARNING: atom H5'1 is missing in residue 2MG 1 in the pdb file
You might need to add atom H5'1 to the hydrogen database of
residue 2MG
in the file ff???.hdb (see the manual)
WARNING: atom H5'2 is
Rui Li wrote:
Dear all,
I want run a Position-restrained dynamics simulation for my system
and I write a pr.mdp file.
below is part of the mdp file:
Berendsen temperature coupling is on in three groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1
tc-grps
Hi Nicolas,
I don't see any warnings concerning bonds, so it seems these are
handled correctly. Check the atom numbers and types of the angles (and
dihedrals) this concerns and try to find out why it doesn't work the
way you want it to ( = homework).
Best,
Tsjerk
On 4/23/07, martinez <[EMAIL P
Hi Martinez,
pdb2gmx doesn't do that for you. grompp does. With the specbond.dat
you let pdb2gmx find the bonds and list them in the topology. When
running grompp, it will apply a default bond/angle/dihedral type for
bonds/angles/dihedrals listed, but for which no parameters are given,
based on t
Rui Li wrote:
Dear all,
I want run a Position-restrained dynamics simulation for my system
and I write a pr.mdp file.
below is part of the mdp file:
Berendsen temperature coupling is on in three groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1
tc-grps
Александр Журавлев wrote:
Hallo Gromacs users! Let me ask you a question. In my ligand-receptor system I
have a special type of interaction between aromatic rings of amono acid and
ligand, that depends significantly on the distance and angle between two
aromatic planes. What type of constrain
Dear all,
I want run a Position-restrained dynamics simulation for my system
and I write a pr.mdp file.
below is part of the mdp file:
Berendsen temperature coupling is on in three groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1
tc-grps = Protein
Hi Martinez,
pdb2gmx doesn't do that for you. grompp does. With the specbond.dat
you let pdb2gmx find the bonds and list them in the topology. When
running grompp, it will apply a default bond/angle/dihedral type for
bonds/angles/dihedrals listed, but for which no parameters are given,
based on t
Thank you for your reply Tsjerk
I have already edited my spec bond.dat file as follows
14
CYS SG1 CYSSG 1 0.2 CYS2
CYS2
CYS SG1 HEME FE 2 0.25 CYS2HEME
CYS SG1 HEME CAB
Hi Nagaraju,
On 4/23/07, naga raju <[EMAIL PROTECTED]> wrote:
Dear gmx users,
I am thankful to Tsjerk Wassenaar and Chris
Neale, to their suggestions. I prepared dopc.itp parameter file for DOPC
lipid bilayer. To Protein+DOPC bilayer system, which force field I have to
Hallo Gromacs users! Let me ask you a question. In my ligand-receptor system I
have a special type of interaction between aromatic rings of amono acid and
ligand, that depends significantly on the distance and angle between two
aromatic planes. What type of constraints should I use in the top
You wouldn't happen to use the AMBER-port and nucleic acids, would
you? In that case you should look out for an issue with the
aminoacids.dat that can cause non integer total charge.
/Erik
23 apr 2007 kl. 11.27 skrev Tsjerk Wassenaar:
Hi Riu Li,
Now, add 0.28 Na+ ion to your system.
Chec
Hi all!
I`m working on tRNA MD. My structure contains modified base 2MG, which have
been added to the ffamber99p.rtp:
[2MG]
[atoms]
P amber99_461.087831
O1P amber99_45 -0.7 2
O2P amber99_45 -0.73
O5' amber99_44 -0.471314
C5' amber99_11
Hi Riu Li,
Now, add 0.28 Na+ ion to your system.
Check your topology, it doesn't add up somewhere. The sum of the
partial charges should be integer (taken into account a rounding
error).
Cheers,
Tsjerk
On 4/23/07, Rui Li <[EMAIL PROTECTED]> wrote:
Dear all,
When I use grompp,it warns:
NOTE:
Dear all,
When I use grompp,it warns:
NOTE:
System has non-zero total charge: 1.172000e+01
So I add 12 Cl- in my system.
Then I use grompp again,it warns:
NOTE:
System has non-zero total charge: -2.799983e-01
How can I make the total charge zero?
_
Dear gmx users,
I am thankful to Tsjerk Wassenaar and Chris Neale,
to their suggestions. I prepared dopc.itp parameter file for DOPC lipid
bilayer. To Protein+DOPC bilayer system, which force field I have to choose to
my protein.
any suggestion
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