On 7/21/13 12:18 AM, Collins Nganou wrote:
Dear Users,
when trying to run the following command:
mdrun -v -deffnm protein-EM-solvated -c protein-EM-solvated.pdb
I have received the error below.
Reading file dna-EM-solvated.tpr, VERSION 4.5.5 (single precision)
Starting 2 threads
--
Dear Users,
when trying to run the following command:
mdrun -v -deffnm protein-EM-solvated -c protein-EM-solvated.pdb
I have received the error below.
Reading file dna-EM-solvated.tpr, VERSION 4.5.5 (single precision)
Starting 2 threads
---
P
On 8/9/12 1:40 PM, Shima Arasteh wrote:
Dear gmx users,
Would be this error (as you see here) a symptom of blowing up of a system? Or
just .mdp options should be changed?
Fatal error:
1 of the 16625 bonded interactions could not be calculated because some atoms
involved moved further apart
Dear gmx users,
Would be this error (as you see here) a symptom of blowing up of a system? Or
just .mdp options should be changed?
Fatal error:
1 of the 16625 bonded interactions could not be calculated because some atoms
involved moved further apart than the multi-body cut-off distance (0.8176
Nilesh Dhumal wrote:
Hello,
I am trying to do equilibration for my system (solvent + solute). I am
geting the following error. If I run solvent and solute molecules
separately, its run well. For mixture I am getting following error.
What this error means.
Fatal error:
1 of the 22334 bonded int
Hello,
I am trying to do equilibration for my system (solvent + solute). I am
geting the following error. If I run solvent and solute molecules
separately, its run well. For mixture I am getting following error.
What this error means.
Fatal error:
1 of the 22334 bonded interactions could not be ca
Cíntia C. Vequi-Suplicy wrote:
Hello Justin,
I used Gromacs 4.0.5 and the error was gone. Thank you.
But now I have another problem when using mdrun_d. I gave the comand:
mdrun_d -s dppc.tpr -o dppc128.trr -c dppc128.gro -g dppc.log &
And first I got a lot of output on the shell window and
Hello Justin,
I used Gromacs 4.0.5 and the error was gone. Thank you.
But now I have another problem when using mdrun_d. I gave the comand:
mdrun_d -s dppc.tpr -o dppc128.trr -c dppc128.gro -g dppc.log &
And first I got a lot of output on the shell window and I think it is
strange. This out
Pawan Kumar wrote:
probably a bad starting structure...
check this website for pressure scaling warning :
http://wiki.gromacs.org/index.php/Errors
Also,
compressibility = 4.575e-4
is of the wrong magnitude for water. Should be e-5.
-Justin
regards,
pawan
On Mon, Apr 27, 2009 a
probably a bad starting structure...
check this website for pressure scaling warning :
http://wiki.gromacs.org/index.php/Errors
regards,
pawan
On Mon, Apr 27, 2009 at 5:21 PM, Sheetal Arora wrote:
> I am trying to run the simulation of protein ligand complex.
> But after running the mdrun by gi
I am trying to run the simulation of protein ligand complex.
But after running the mdrun by giving command-"grompp –f md.
mdp –c pr.gro –p trp.top –o md.tpr "
and then "nohup mdrun –deffnm md & "
the md.log file is showing the following message-
Step 11 Warning: pressure scaling more than 1%, mu:
supti mukherjee wrote:
Dear all,
I am doing a protein simulation for 20ns in single processor machine.
You may wish to avoid using MPI versions of GROMACS on a
single-processor machine.
after 11.1ns when I am trying to rerun mdrun its coming out with the
following error.
-
Dear all,
I am doing a protein simulation for 20ns in single processor machine. after
11.1ns when I am trying to rerun mdrun its coming out with the following
error.
--
Inner product between old and new vector <= 0.0!
constraint #0 atoms 1 and 2
Warning: 1-4 inte
hi
i tried to run the simulation with single alamethicin molecule but i am getting
the same error as i was getting earlier.
Warning: 1-4 interaction between 164 and>> 169 at distance 3.430 which is
larger than the 1-4 table size 1.000 nm.
I used the command
$ genbox -cp alamethicin.gro -cs po
pragya chohan wrote:
Hi justin
I placed POPC membrane in a box too of same dimension as the box of
alamethicin and centred it too so that alamethicin is placed correctly
in the membrane.
I am attaching the pdb please have a look.
Any help would be appreciated
Check out http://wiki.gromacs.or
gt;
> -Justin
>
> >
> > Pragya
> >
> >
> >
> > > Date: Sat, 10 Nov 2007 12:42:01 -0500> From: [EMAIL PROTECTED]> To:
> > gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Quoting
> pragya
> > chohan <[EMAIL PROTE
>
> > Date: Sat, 10 Nov 2007 12:42:01 -0500> From: [EMAIL PROTECTED]> To:
> gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Quoting pragya
> chohan <[EMAIL PROTECTED]>:> > > Thanks Justin for your reply. I am
> generating the start
; From: [EMAIL PROTECTED]> To:
> gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Quoting pragya
> chohan <[EMAIL PROTECTED]>:> > > Thanks Justin for your reply. I am
> generating the starting structure through> > genbox.> > I adde
tively, you can use make_hole.pl or the inflategro script available
through Peter Tieleman's site:
http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis
-Justin
>
>
> > Date: Sat, 10 Nov 2007 10:22:45 -0500> From: [EMAIL PROTECTED]> To:
> gmx-users@gromacs.org>
10:22:45 -0500> From: [EMAIL PROTECTED]> To:
> gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Since
> alamethicin works on its own, it suggests to me that the introduction of>
> alamethicin into POPC is what's causing the problem, and judging by the&
Since alamethicin works on its own, it suggests to me that the introduction of
alamethicin into POPC is what's causing the problem, and judging by the
enormous potential energies and forces, it appears to be bad contacts/atomic
overlap (at least, that's been the cause of problems in my experience).
> Date: Fri, 9 Nov 2007 09:01:48 -0500>
From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users]
mdrun error>> Check out the wiki at:>>
http://wiki.gromacs.org/index.php/Errors#LINCS_warnings>> Alternativ
>
> hi i am trying to run mdrun for protein in membrane system. When i run
> mdrun i get a warning
Check out the wiki link Justin provided. Also read
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation and make
sure your setup regime is reasonable.
Also, when you run grompp, pay atten
Check out the wiki at:
http://wiki.gromacs.org/index.php/Errors#LINCS_warnings
Alternatively, search the list for some of my posts from around a year ago - NVT
and minimization of a lipid bilayer (or search for my name, they should come up
as well). I suspect you have bad contacts in your starti
hi i am trying to run mdrun for protein in membrane system. When i run mdrun i
get a warning
Step -2, time -0.002 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 2.144082 (between atoms 12433 and 12434) rms 0.216090
bonds that rotated more than 30 degrees:
atom 1 atom 2 angl
Blaise Mathias-Costa wrote:
Hello Mark and Tsjerk, Thanks a lot for your suggestions. I have gone
through that web site and it doesn't say anything very specific, for
example if the system is not minimized properly it should have
complained at the beginning, but the problem arises after 2.6nS!
a, PhD
> Department of Pharmacology and Experimental Neuroscience
> University of Nebraska Medical Center
> Omaha, NE 68198-5800, USA.
> Tel: 001 402 559 7132
>
> [EMAIL PROTECTED] wrote: -
>
> To: Discussion list for GROMACS users
> From: Mark Abraham <[EMAIL PROTECTE
on list for GROMACS users From: Mark Abraham <[EMAIL PROTECTED]>Sent by: [EMAIL PROTECTED]Date: 10/02/2007 12:29PMSubject: Re: [gmx-users] mdrun error after 2.6nSBlaise Mathias-Costa wrote:> Hi all,> > The mdrun stopped after 2.6nS after writing this error:> Step 132157
Blaise Mathias-Costa wrote:
Hi all,
The mdrun stopped after 2.6nS after writing this error:
Step 1321571, time 2643.14 (ps) LINCS WARNING
See http://wiki.gromacs.org/index.php/Errors#LINCS_warnings
Mark
___
gmx-users mailing listgmx-users@gro
Hi Blaise,
You'd better look in the log file where this starts. I bet it's either
Lys-NH3+ or phosphate (ATP?) spinning like crazy. Check the archive for
solutions.
Best,
Tsjerk
On 10/2/07, Blaise Mathias-Costa <[EMAIL PROTECTED]> wrote:
>
> Hi all,
>
> The mdrun stopped after 2.6nS after wri
Hi all,The mdrun stopped after 2.6nS after writing this error:Step 1321571, time 2643.14 (ps) LINCS WARNINGrelative constraint deviation after LINCS:max 2.814066 (between atoms 2742 and 2745) rms 0.041434bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint
Hi,
What's settings for tc-grps, tau_t and ref_t in your mdp files?
Regards,
Yang Ye
On 1/2/2007 8:59 PM, Dhananjay wrote:
Hello all,
I have minimized the pdb file and wish to do mdrun for position
restrain dynamics.
For this when I run grompp programm, it is showing error as follows. I
do
Hi Dhananjay,
Happy new year :)
Just what it says: not enough ref_t and tau_t values. You use
"Protein" and "Sol" as temperature coupling groups, but likely, you
also have ions in your system, which are not coupled now. You may want
to use "Protein" and "Non-Protein" in stead. In case you have s
Hello all,
I have minimized the pdb file and wish to do mdrun for position restrain
dynamics.
For this when I run grompp programm, it is showing error as follows. I don't
understand why it is showing this error:
processing coordinates...
double-checking input for internal consistency...
Velociti
: David van der Spoel <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Date: Thu, 15 Jun 2006 12:00:35 +0200
Subject: Re: [gmx-users] mdrun error
> Mahnam wrote:
> >
> > In God We Trust
> > Hi Dr Biswas
> > Thank you for your guids.Excuse me for many q
Mahnam wrote:
In God We Trust
Hi Dr Biswas
Thank you for your guids.Excuse me for many question. I am using a
serial version of CPMD. I made cpmdmpi script and corrected the path of
cpmd.x ( /root/CPMD-3.11.1/SOURCE/cpmd.x CPMD_inp.run.),but when I run
rgmx script , mdrun says:
GROMACS aw
In God We Trust
Hi Dr Biswas Thank you for your guids.Excuse me for many question.
I am using a serial version of CPMD. I made cpmdmpi script and corrected the
path of cpmd.x ( /root/CPMD-3.11.1/SOURCE/cpmd.x CPMD_inp.run.),but
when I run rgmx script , mdrun says: GROMACS awaits
QM-result fo
Hi Maham,
You need to edit the script 'cpmdmpi' so that it does have the path to access the cpmd.x from your working folder. The error message is due to that; it is not being able to access cpmd.x.
1. If you are using a serial version of CPMD then create a script 'cpmdmpi' with the following line
In God We Trust
Hello Dr Biswas Yes, our run created the
output.pdb2gmx, output.grompp_em and output.mdrun_em. Output.pdb2gmx and
output.grompp_em haven't any error message but output.mdrun_em has an
error .I attached it to this mail. Thank you very much in advance
for your kindness and yo
Hi gmx-users,
I am setting up a membrane inserted protein simulation.
The protein is mutated at a specific place and attached to a label and
this is inserted into the POPC membrane (434 lipids). The label is a
small molecule whose force field params were generated on PRODRG
server.
Everything was
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