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
---
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
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
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
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
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
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
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:
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
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
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
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 Alternatively, search
the list for some of my
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
: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
enormous potential energies and forces
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 Subject: RE: [gmx-users] mdrun error Since
alamethicin works on its own, it suggests
: [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 added popc as
solvent around alamethicin after aligning alamethicin in a box
: [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 added popc as
solvent around alamethicin after aligning alamethicin in a box
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 Subject: RE: [gmx-users] mdrun error Since
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
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
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
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
cs.orgFrom: 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 1321571, time 2643.14 (ps) LINCS WARNINGSee http://wiki.g
: 001 402 559 7132
[EMAIL PROTECTED] wrote: -
To: Discussion list for GROMACS users gmx-users@gromacs.org
From: Mark Abraham [EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]
Date: 10/02/2007 12:29PM
Subject: Re: [gmx-users] mdrun error after 2.6nS
Blaise Mathias-Costa wrote:
Hi all
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!
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 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 writing
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...
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 some non
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 for
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
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
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
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