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Hello;
I took 2000 configuration from trajconv. Amino acid is in its normal shape
till almost conf1000.gro(and a little more). But in for example
conf1300.gro amino acid was disintegrated. What does it mean? Would you
please help me?
Best regards
Rose
On Sun, Nov 26, 2017 at 12:39 AM, Justin Lem
Dear Justin
It worked. Actually by its own. I reconstructed the pdb and gave again.
Thank you so much for your time
On Tue, Nov 28, 2017 at 10:08 AM, RAHUL SURESH
wrote:
> This error occur only for this particular pdb structure. The protein here
> is attached with a metal ion. The necessary ch
This error occur only for this particular pdb structure. The protein here
is attached with a metal ion. The necessary changes are made to the
charmm36 ff.
Should be some error in my pdb?
On Tue, Nov 28, 2017 at 10:04 AM, RAHUL SURESH
wrote:
> Here i have added the report for the commands
>
>
>
Here i have added the report for the commands
Command line:
*gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*
Read 628 atoms
Volume: 579.929 nm^3, corresponds to roughly 260900 electrons
No velocities found
system size : 3.716 91.693 1.702 (nm)
diameter: 91.698
On 11/27/17 3:12 PM, Saumyak Mukherjee wrote:
Dear Justin,
Thanks for the reply.
In that case, if I want the SOL-Backbone interaction energy, how shall I
choose the energygrps? Is it possible to have such a group in the index.ndx
file?
You have to have fully intact charge groups, which mean
Dear Justin,
Thanks for the reply.
In that case, if I want the SOL-Backbone interaction energy, how shall I
choose the energygrps? Is it possible to have such a group in the index.ndx
file?
Regards,
Saumyak
On 27 November 2017 at 19:05, Justin Lemkul wrote:
>
>
> On 11/27/17 5:25 AM, Sau
Thank you :)
On Sun, Nov 26, 2017 at 11:36 PM, Dallas Warren
wrote:
> You can do whatever you want, and there are many tools to help you do that.
>
> Couple of options are using gmx insert-molecules (constrain the box
> size to make the film, then enlarge afterwards to insert other
> molecules),
On 11/27/17 11:26 AM, RAHUL SURESH wrote:
Hi
*gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*
And how large is the resulting box? Are all the coordinates properly
defined? What is the full screen output of gmx solvate up to the failure?
-Justin
I have used the above command t
On 26/11/17 17:08, Rakesh Pant wrote:
Dear Alex,
But g-x2top doesn't work till we define all atom types in .n2t file.
Please do not use this at all. Use acpype or something.
Thanks
On 26-Nov-2017 9:34 PM, "Alexandr Nasedkin" wrote:
Hi,
You will need to have both ffbonded.itp and ffnonbo
Dear community,
I share the results of scaling- performance test. I used this command and
checked the core usage with the help of htop tool (http://hisham.hm/htop/):
gmx mdrun -ntmpi 1 -ntomp N -pin on -deffnm &
Where N is the number of (logical) cores, and hardware is Intel(R) Core(TM)
i7-67
Hi
*gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*
I have used the above command to generate the box. Infact I have used this
command before and I never got any error.
Thank you
On Mon, Nov 27, 2017 at 7:07 PM, Justin Lemkul wrote:
>
>
> On 11/27/17 7:17 AM, RAHUL SURESH wrote:
>
>
Thanks for correcting..
On Mon, Nov 27, 2017 at 7:02 PM, Justin Lemkul wrote:
>
>
> On 11/27/17 1:02 AM, Tasneem Kausar wrote:
>
>> pKa of amino acid residue is a constant quantity. Depending on the pH you
>>
>
> That's not strictly true. Titratable amino acids can be found in unique
> micro
Dear Gromacs Users,
I need the SPC/Fw model of water. Could I receive this model?
Best Regards
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On 11/27/17 7:17 AM, RAHUL SURESH wrote:
Dear Users
I am trying to carryout protein-metal interaction using charmm36 ff. During
solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o solv.gro"
*i receive a error stating
*"Fatal error:Not enough memory. Failed to realloc 3094
On 11/27/17 6:04 AM, GIANMARCO BARTALINI wrote:
Hello guys, I produced a system "protein + lipid membrane" using the online
tool CHARMM-GUI. Since I need to use the Amber force field, I added the
Lipids17 force field inside Gromacs. The implementation should work fine,
since the conversion of a
On 11/27/17 5:25 AM, Saumyak Mukherjee wrote:
Dear All,
I want to calculate the interaction energy between water and protein
backbone. However, in mdp file, when I am using
energygrps = SOL backbone
grompp is returning the following error.
Fatal error:
atoms 1 and 2 in charge group 1 of mo
On 11/27/17 1:04 AM, atb files wrote:
Dear Users,When there is a Lincs warning (sometimes because of exceeding warnangle etc) the gromacs generates pdb files. My questions is:What is purpose of generating pdb files? What information they give? Which information
On 11/27/17 1:02 AM, Tasneem Kausar wrote:
pKa of amino acid residue is a constant quantity. Depending on the pH you
That's not strictly true. Titratable amino acids can be found in unique
microenvironments that cause shifts in canonical values. For instance,
there are some catalytic lysine
On 11/26/17 11:09 PM, za...@tezu.ernet.in wrote:
Hello Everyone
I am trying to simulate a protein at two pH (7.4 and 9.0) using
gromacs 5.1.4. The protein has no missing residues. Optimal pH range is
6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17
positively charged residu
Dear Users
I am trying to carryout protein-metal interaction using charmm36 ff. During
solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o solv.gro"
*i receive a error stating
*"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes for
atoms_->atom,atoms_->atom=0(
Hello guys, I produced a system "protein + lipid membrane" using the online
tool CHARMM-GUI. Since I need to use the Amber force field, I added the
Lipids17 force field inside Gromacs. The implementation should work fine,
since the conversion of an equilibrated structure produces a nice and
correct
Dear Gerrit,
Thank you very much for your prompt reply.
I’ve tried to run the simulation with wenjin’s tutorial and it passed the point
charge correction step with no problem. I compared the “.out” output files of
my protein and of the tutorial peptide, I noticed there’s a line “%pointcharges
“
Dear All,
I want to calculate the interaction energy between water and protein
backbone. However, in mdp file, when I am using
energygrps = SOL backbone
grompp is returning the following error.
Fatal error:
atoms 1 and 2 in charge group 1 of molecule type 'Protein_chain_A' are in
different ene
>From the error message it seems that ORCA program crashes. Unfortunately, Orca
>is no longer supported, which means that if the ORCA's input or anything else
>has changed, the gromacs interface may fail.
What you could try is to use the version of ORCA that others have used before.
Best,
Gerr
Hi,
There's some useful background at
http://manual.gromacs.org/documentation/2016.4/user-guide/mdrun-performance.html
Whether you want mpirun -np X mdrun_mpi or mpirun -np X gmx_mpi mdrun
depends whether GROMACS was configured to build only mdrun.
Otherwise, the logfile is indeed your friend -
On 27/11/2017 07:21, Ali Ahmed wrote:Hello GMX users
I'm trying to do simulations on multi nodes so I used 8 nodes (128
processors). AS I see there is no difference between 1 node and 8 nodes.
Check the log file showing how many nodes you use, look for a line as in
template:
Running on 2 nodes
Dear Gromacs Users,
I've been running a QM/MM calculation on a protein with fluorescence probe,
using gromacs 4.6.7 (double precision with MPI) and ORCA 4.0.1. The following
lines were included in the .mdp file,
QMMM = yes
QMMM-grps= QMatoms
QMmethod
Dear Users,When there is a Lincs warning (sometimes because of
exceeding warnangle etc) the gromacs generates pdb files. My questions is:What
is purpose of generating pdb files? What information they give? Which
information we need to look for to analyse those pdb
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