Many thanks Alex for your reply :)
You have pressure scaling and LINCS convergence issues, suggesting that
> the starting configuration is far from equilibrium, as well as
> potentially other issues.
>
> How to check if my starting configuration is far from equilibrium ? I
checked the Temperature
You have pressure scaling and LINCS convergence issues, suggesting that
the starting configuration is far from equilibrium, as well as
potentially other issues.
Gromos FF is not appropriate for graphene, and neither is turning C-C
bonds into LINCS constraints, as set by your 'all-bonds' -- gra
Dear Gromacs users
I am using amber99sb-ildn.ff force field for protein and I used GAFF for
ligand parameterization.
I tried different options e.g using constraint =all bonds as well as
h-bonds. Reducing the time step to 1 fs but still, I could not solve the
problem and get lincs warning production
Hi Afsane,
This might be an issue with the pressure coupling, depending on the
compressibility you give for your system and the algorithm that you use
for pressure coupling you might see quite large fluctuations in
pressure. One idea might be to use temperature coupling to quickly
dissipate
Hi Afsane,
You need to provide more details of the simulation, such as how you generated
the configuration and topology, what force field you used and so on, or we can
not give you any advice.
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China.
Zip: 2
Check the forcefield you are using is appropriate for your system or there
might be some problem with the ligand parameters.
On Tue, Mar 24, 2020 at 11:30 AM Sadaf Rani wrote:
> Dear Gromacs users
> I ran an MD simulation for 3ns and from the last coordinates started a free
> energy calculation
Dear Mark
Thank you for your reply
I resolved my problem by refining the output ot the tool
Best
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Hi,
I can't tell whether that's a periodicity artefact in your visualization,
or the topology is indeed junk. You will likely need to inspect the output
of the tool that generated it. Rarely do these things "just work."
Mark
On Sun, Nov 11, 2018 at 3:01 AM Farial Tavakoli
wrote:
> Dear Mark
>
Dear Mark
Thank you for your reply
I got dt=0.5 ps and run EM and NVT on the ligand in vacuo and got this
results:
EM results:
Steepest Descents converged to machine precision in 80 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = -3.4145945e+03
Maximum force = 6.6
Hi,
That tends to suggest either your ligand conformation or ligand parameters
are not appropriate. What happens with ligand in vacuo with EM and then NVE
with a very small time step, e.g. 0.5 ps?
Mark
On Sat, Nov 10, 2018 at 10:50 AM Farial Tavakoli
wrote:
> Dear gromacs users
>
> I am tr
Hi,
Simplify things until you identify the problematic part. Eg do one CO2
molecule first.
Mark
On Thu, 19 Oct 2017 03:16 Pimo Oni wrote:
> Dear community members,
>
> Recently I'm using GMX 5.1.4 to simulate EPM2 CO2 with virtual sites, while
> I met continual LINCS WARNING. I've been struggl
On 8/2/17 9:12 AM, Ali Ahmed wrote:
Dear all,
Thank you for helping me. All I get from grompp is this
--
gmx grompp -f grompp.mdp -c N2_box.gro -po mdout.mdp -p topol.top -o
topol.tpr
Ignoring obsolete mdp entry 'title'
Ignor
Dear all,
Thank you for helping me. All I get from grompp is this
--
gmx grompp -f grompp.mdp -c N2_box.gro -po mdout.mdp -p topol.top -o
topol.tpr
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Back Off!
On 8/1/17 6:07 PM, Ali Ahmed wrote:
Dear Dr. Dallas,
Thank you for your reply. Actually, I'm new to GROMACS and
I appreciate your support.
Dear Dr. Dallas,
Thank you for your reply. Actually, I'm new to GROMACS and
I appreciate your support.
--
Here is what I get be
Copy the output from both of those commands, most importantly (as Mark
has asked) that from the first one gmx grompp
You need to show people exactly what you are seeing, not what you say
you are seeing. The latter you are filtering it, and most likely not
providing all the important information.
Hi,
Thank you for your help.
well I used this command
gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em
and I got all the warnings. Here is my em.mdp
-
integrator = steep
em
Hi,
No, only mdrun issues LINCS warnings. grompp issues different warnings, and
I would like you to check whether you had any from grompp that you may not
have considered. :-)
Mark
On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed wrote:
> Dear Mark
> Yes, all the warnings are from grompp.
> I have no
Dear Mark
Yes, all the warnings are from grompp.
I have no idea where is the problem in the structure or the topology
Thank you
On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham
wrote:
> Hi,
>
> Did you get any warnings from grompp?
>
> Mark
>
> On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed wrote:
>
>
Hi,
Did you get any warnings from grompp?
Mark
On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed wrote:
> Hello GROMACS users,
>
> I'm doing MD for nitrogen, and for better electrostatic interactions I need
> to use massless and charged virtual site. I did that but when I try to do
> energy minimizati
Dear Mark,
I understand your point,
but I've used the Martini-backmapping protocol written in the initram.sh
wrapper found in Martini documentation
(https://github.com/Tsjerk/MartiniTools/blob/master/initram.sh), so it
seems to me quite weird that it was not working in the proper manner.
an
Hi,
I would avoid using the combination of position restraints and constrained
bonds with an input structure that is not necessarily consistent with the
constraints. That's a recipe for large forces. I wouldn't use position
restraints in such a process unless I had some reason to believe that my
s
hi,
I've seen with vmd the gro file generated after the transformation, and
after the 2 steps of minimization,
it seems that they have no problem,
while if I see the step_n.pdb file generated before the crash, there are
some atoms far away from the rest of the protein, while this is not
happe
Hi,
Those are all good things, but have you actually got out a molecular viewer
and looked at the input and output of your resolution conversion?
Mark
On Wed, Jul 12, 2017 at 4:25 PM edesantis wrote:
> Hi,
> thanks for the prompt answer,
>
>
> I've found the same problem even if I try to conve
Hi,
thanks for the prompt answer,
I've found the same problem even if I try to convert the coarse grained
pdb obtained from martinize.py, so in that case it should be not a
problem to have the conversion, for this reason I though it is a
methodological problem...
I've seen the blowing-up is
Hi,
Sounds like you might be
http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the
conversion doesn't work for your configuration. You should start by doing a
visual check of the configuration for sanity, then follow the advice in
that link.
Mark
On Wed, Jul 12, 2017 at 3:04 PM
On 3/14/17 2:57 AM, fatemeh ramezani wrote:
Dear gmx usersplease help me if you know how can I change lincs warning
threshold in mdp file or in command?
The .mdp option is lincs-warnangle but you should not be toying with this option
just to make errors go away; LINCS warnings indicate a s
On 8/25/16 5:56 AM, amitbe...@chemeng.iisc.ernet.in wrote:
Hello users,
I was trying to energy minimize my system of protein embedded in bilayer.
But I am receiving the following error:
Step -1, time -0.001 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000942, max 0.1490
Dear Sir,
I have used 1.8 rdd value.
Kind Regards,
Antara
--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi - 110020
M : +91-9717970040
--
On Sat, May 14, 2016 at 12:14 AM, subhadip das
wrote:
> Can you tell me
Hi Antara,
What commands did you use? At least make sure you add -rdd 1.6 to the
command line of mdrun, because the default value is too small for coarse
grain simulations.
Cheers,
Tsjerk
On Fri, May 13, 2016 at 8:12 PM, Antara mazumdar
wrote:
> Dear users,
>
> I am trying to run a coarse gra
Dear users,
I am trying to run a coarse grained simulation of a membrane protein in a
mixed lipid billayer using martini model 2.2. I have already performed all
the equilibration steps successfully on my desktop with GROMACS 5.1.0.
However, when i try to execute its production run in parallel(havi
Hi,
Several things will make it easier to help - particularly your GROMACS
versions and how you ran mdrun. See also http://www.gromacs.org/Support
Mark
On Fri, May 13, 2016 at 7:42 PM Antara mazumdar
wrote:
> Dear gromacs users,
>
> I am trying to run a coarse grained simulation of a membrane
Dear Justin,
I am so thankful for you kindly reply. Now, I can solve this problem.
Tuong Vy
On Tue, Oct 6, 2015 at 11:49 PM, Justin Lemkul wrote:
>
>
> On 10/6/15 3:26 AM, Vy Phan wrote:
>
>> Dear all gromacs Users!
>> I want to run a simulation with the system protein-ligand (I have several
>>
On 10/6/15 3:26 AM, Vy Phan wrote:
Dear all gromacs Users!
I want to run a simulation with the system protein-ligand (I have several
ligands).
With EM, nvt, npt step I put position restraint for the ligands and all
thing was fine. After that, I run production simulation without position
restrai
On 7/14/15 3:07 AM, Sun Iba wrote:
Hello Everyone
I am simulation a protein as per the lysozyme tutorial. MY simulation got
dumped at final mdrun step. It is showing following warning :
Command line:
gmx mdrun -deffnm md_0_1
Reading file md_0_1.tpr, VERSION 5.0.5 (single precision)
Using 1
On 4/28/14, 1:37 AM, Gaurav Saraf IDD M Tech Biochem. Engg, IIT (BHU) wrote:
Dear Gromacs user,
After I give the command for nvt, I get the following error:
starting mdrun 'Protein in water'
15 steps,300.0 ps.
Step 0, time 0 (ps) LINCS WARNING
If the run crashes at step zero, it su
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