Probably the default behaviour of pdb2gmx for termini is not appropriate
for your input. Use pdb2gmx -ter and choose wisely
Mark
On Nov 13, 2013 12:03 PM, "hasthi" wrote:
> Hello GROMACS users,
> I have phosphorylated Serine residue in my
> protein (140 residues) of
On 11/13/13 6:02 AM, hasthi wrote:
Hello GROMACS users,
I have phosphorylated Serine residue in my
protein (140 residues) of interest, now when I run pdb2gmx I get this
following error
Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms
while
Hello GROMACS users,
I have phosphorylated Serine residue in my
protein (140 residues) of interest, now when I run pdb2gmx I get this
following error
Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms
while sorting atoms.
I checked aminoacid.rtp,
On 11/7/13 6:27 AM, Arunima Shilpi wrote:
Dear Sir
Presently I am working with the example file as given in the umbrella
sampling tutorial.
While running the following command
grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr
I got the following error. How to debu
Dear Sir
Presently I am working with the example file as given in the umbrella
sampling tutorial.
While running the following command
grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr
I got the following error. How to debug this error.
Ignoring obsolete mdp entry 't
On 10/27/13 11:23 AM, sunyeping wrote:
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
--
发件人：Justin Lemkul
发送时间：2013年10月27日(星期日) 20:27
收件人：gromacs
主 题：Re: 答复: [gmx-users] error in umbralla sampling step 6
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
--
发件人：Justin Lemkul
发送时间：2013年10月27日(星期日) 20:27
收件人：gromacs
主 题：Re: 答复: [gmx-users] error in umbralla sampling step 6
Please keep the discussion on the list.
On
Please keep the discussion on the list.
On 10/27/13 5:09 AM, sunyeping wrote:
Dear professor Lemkul,
For warning 1:
I use the npt_umbrella.mdp file you provided in step 6 in the umbralla sampling
tutorial. You told us to start by running a brief NPT equilibration in each
window using this mdp
On 10/26/13 10:45 AM, sunyeping wrote:
Dear gromacs user,
I am doing umbralla sampling on a protein-ligand system following the gromacs
umbralla sampling turial. It seems that the first five steps go well, and I
select 23 gro files as the starting configurations of adjacent umbrella
sampling
Dear gromacs user,
I am doing umbralla sampling on a protein-ligand system following the gromacs
umbralla sampling turial. It seems that the first five steps go well, and I
select 23 gro files as the starting configurations of adjacent umbrella
sampling windows. However when I use grompp to gene
Look at the numbers, count the number of atoms you expect in each
moleculetype, and work out what the mismatch is.
Mark
On Wed, Sep 18, 2013 at 2:58 PM, naresh_sssihl wrote:
> Dear GMX users,
>
> I am trying to simulate a protein in SDS/Water box.
>
> 1. No problems with pdb2gmx - .gro file and
Dear GMX users,
I am trying to simulate a protein in SDS/Water box.
1. No problems with pdb2gmx - .gro file and .top files were generated.
/pdb2gmx -f protein.pdb -o protein_pro.gro -water spce/
selected ff 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
2. Created a Cubic box usin
On Wed, Sep 11, 2013 at 3:08 PM, Mark Abraham wrote:
> No idea if it's causing your problem, but you need all the Ds in
> -DBUILD_SHARED_LIBS=no
>
> Mark
>
> On Wed, Sep 11, 2013 at 6:15 AM, Qin Qiao wrote:
> > Dear all,
> >
> > I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local clu
If the version of gcc is unsuitable, you can write the path to it in
gold leaf and it still won't help :-) Check gcc --version for the
exercise, and then find out how to install 4.7.x or 4.8.x.
Mark
On Wed, Sep 11, 2013 at 5:09 AM, Golshan Hejazi
wrote:
>
>
> Hello,
>
> i am trying to compile gr
No idea if it's causing your problem, but you need all the Ds in
-DBUILD_SHARED_LIBS=no
Mark
On Wed, Sep 11, 2013 at 6:15 AM, Qin Qiao wrote:
> Dear all,
>
> I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster
> and got the following error in step 'make':
>
> "/usr/bin/ld:
>
Dear all,
I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster
and got the following error in step 'make':
"/usr/bin/ld:
/usr/local/mvapich2-1.9a-gcc/lib/libmpich.a(mvapich_malloc.o): relocation
R_X86_64_32 against `.bss' can not be used when making a shared object;
recompile
Hello,
i am trying to compile gromacs-4.6.1 on a linux machine. I used already the
following compile script and it worked
export CCDIR=/usr/bin/gcc
export MPICCDIR=/usr/mpi/gcc/openmpi-1.4.1/bin
export CXX=mpicxx
export CC=mpicc
cd /home/fbafti/CODE
tar -xvf gromacs-4.6.1.tar.gz
cd mv gr
Hi Dear Gromacs users,
I would like to calculate the standard deviation (as the error bar) for
dV/dlambda.xvg file. I used g_analyze command as the following:
g_analyze -ffree0.9.xvg -av average_0.9
I got:
set average*standard deviation**std. dev. /
sqr
Hi Sri,
I guess that this simulation was run through the WeNMR GMX portal? It's not
really a Gromacs question. Problems with that portal should be directed to
the adminstrator, who will send it to me anyway, so I'll respond here :)
The error means 1. that I should put time in writing more clear e
Dear Gromacs ,
I running the md simulation for protein complex (44 kd ) with amber99sb-ildn
force filed . iam getting error as follows , looks like it is syntax error .
Input file: gmx-495644.pdb Base name: gmx-495644 Source directory:
/scratch/home/enmr028/home_cream_840250368/CREAM840250368 GR
On 8/26/13 4:05 PM, chinnu657 wrote:
Hello all, I am trying to find the distance between 2 centres of mass using
g_dist.
I use the command: g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n
index.ndx
but i get the error:
Fatal error:
Molecule in topology has atom numbers below and above nato
Hello all, I am trying to find the distance between 2 centres of mass using
g_dist.
I use the command: g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n
index.ndx
but i get the error:
Fatal error:
Molecule in topology has atom numbers below and above natoms (1707).
You are probably trying to use
genion? Does the following work?
echo 13 | genion -s ion.tpr -o fws-b4em.gro -neutral -conc 0.15 -p fws.top -g
ion.log
-Justin
Message: 2
Date: Thu, 20 Jun 2013 17:57:28 +
From: Raji Viswanathan
Subject: [gmx-users] Error while using genion
To: "gmx-users@gromacs.org"
On 6/20/13 1:57 PM, Raji Viswanathan wrote:
I am new Gromacs user and I found Dr. Kerrigan's tutorial on the spider toxin
peptide. I was going through the steps in the tutorial but got stuck with the
genion command. When I am prompted to select a group, I get the error that it
is not found
I am new Gromacs user and I found Dr. Kerrigan's tutorial on the spider toxin
peptide. I was going through the steps in the tutorial but got stuck with the
genion command. When I am prompted to select a group, I get the error that it
is not found. I tried many different ways of specifying thi
Dear Justin,
thank you for your reply.
Yes, you are right , I have corrected it already and now it works well.
Cheers,
Safa
On 11 June 2013 09:53, Justin Lemkul wrote:
>
>
> On 6/10/13 8:51 PM, Souilem Safa wrote:
>
>> Dear gromacs users,
>>
>> I'm trying to simulate a single molecule in cycloh
On 6/10/13 8:51 PM, Souilem Safa wrote:
Dear gromacs users,
I'm trying to simulate a single molecule in cyclohexane.
I made a box of my molecule using editconf command and next I solvate with
cyclohexane using genbox command :
genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o chx_DRG.gro
Dear gromacs users,
I'm trying to simulate a single molecule in cyclohexane.
I made a box of my molecule using editconf command and next I solvate with
cyclohexane using genbox command :
genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o chx_DRG.gro
I did next a position restraint in the top
Use gmxcheck to find out what's in the files. Think about how you used
xtcgroups. Consider using tpbconv to make a matching subset from your .tpr.
Mark
On Wed, May 22, 2013 at 11:53 AM, Arunima Shilpi wrote:
> Respected sir
>
> I want to calculate the distance between protein and ligand after I
Respected sir
I want to calculate the distance between protein and ligand after I have
run the production step. I used the following command..
g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx
Groups I selected was
Group 1 (protein)
Group 13 (ligand)
It says the following error
Mole
Hello,
> Hi all,
>
> I need to do simulation which same as protein-ligand tutorial by Justin.
> The different is i'm using my protein and the ligand was zinc.
> I already follow everything in that tutorial and suddenly when i want
> to heat my protein by using the nvt.mdp there was an error state
Hi all,
I need to do simulation which same as protein-ligand tutorial by Justin.
The different is i'm using my protein and the ligand was zinc.
I already follow everything in that tutorial and suddenly when i want
to heat my protein by using the nvt.mdp there was an error state like
below :
Fatal
On 5/8/13 8:16 AM, Arunima Shilpi wrote:
Hello Sir
While running command for perl distances.pl.. system gets hanged...while
processing particular group file...
I will be thankful to you if you can guide me in debugging the error
If you created groups.txt in accordance with what the tutori
Hello Sir
While running command for perl distances.pl.. system gets hanged...while
processing particular group file...
I will be thankful to you if you can guide me in debugging the error
--
Thanking You with Regards.
Arunima Shilpi
Ph. D Research Scholar(Cancer & Epigenetics)
Department of
Hello sir
While runnimg command for "perl distance.pl" in umbrella sampling it gives
the following error
"Use of uninitialized value $distance in concatenation (.) or string at
distance.pl line 30.
readline() on closed filehandle IN at distance.pl line 16."
Can you guide me in rectifying th
The problem was solved by adding -pbc mol -ur compact flags to the trjconv.
So the problems were indeed in pbc conditions
James
2013/5/3 Mark Abraham
> On Fri, May 3, 2013 at 3:17 PM, James Starlight >wrote:
>
> > Mark,
> >
> >
> > but if I run npt equilibration onto minimized structure (with
On Fri, May 3, 2013 at 3:17 PM, James Starlight wrote:
> Mark,
>
>
> but if I run npt equilibration onto minimized structure (without
> velocities) without definition of the new velocities in the npt.mdp file
>
> gen_vel = No
>
> I noticed that in npt.gro file velocities present. Have it been ass
Mark,
but if I run npt equilibration onto minimized structure (without
velocities) without definition of the new velocities in the npt.mdp file
gen_vel = No
I noticed that in npt.gro file velocities present. Have it been assigned
inspite on
gen_vel = No in mdp?
James
2013/5/3 Mark Abraham
EM has no velocities, by definition. Does the EM mdrun write a .gro file
with velocities? If so, that's a bug.
On Fri, May 3, 2013 at 2:51 PM, James Starlight wrote:
> I've noticed that the minimized conformers no longer has the velocities in
> gro file (and npt rus without warnings in that case
I've noticed that the minimized conformers no longer has the velocities in
gro file (and npt rus without warnings in that case) in comparison to the
not-minimized structures ( where velocities were present and gromp sent
warnings). All pbc options lare the same for all conformers and box vectors
co
On Fri, May 3, 2013 at 11:15 AM, James Starlight wrote:
> Mark,
>
> thanks for suggestions
>
> as I've told previously I've removed pbc via trjconv witout -pbc mol and
> -pbc
> nojump flags
I didn't see anything like that in this thread...
> (the same way I found in Justin's umbrella tutorial
Mark,
thanks for suggestions
as I've told previously I've removed pbc via trjconv witout -pbc mol and -pbc
nojump flags (the same way I found in Justin's umbrella tutorial where
conformers were extracted from pulling trajectory). Might it be source of
the some artifacts with pbc ?
so if I unders
Trajectory frames written by mdrun are not post-processed to guess how you
would like PBC to be treated for whatever purpose you have next. So if a
molecule straddles a periodic boundary given the current center position,
that's what it looks like. If there are things you want to do, then there's
t
Dear Gromacs users!
I have performed long md run. From the production trajectory by means of
trjconv -f md_.trr -s cam.tpr -dt 10 -e 300 -sep -o ./pdbs/.pdb # extract
conformers from first 300 ps each 10ps steps
I've extracted 10 conformers in the desired time step
Than when I perform MD on
On 4/30/13 6:10 AM, Nikunj Maheshwari wrote:
Thanks Justin. I know that using -ignh will solve the problem. But I was
just curious because I got the same error message ("Fatal error: Atom HD1
in residue HIS 65 was not found in rtp entry HISE with 17 atoms while
sorting atoms. ") when I used OPL
Thanks Justin. I know that using -ignh will solve the problem. But I was
just curious because I got the same error message ("Fatal error: Atom HD1
in residue HIS 65 was not found in rtp entry HISE with 17 atoms while
sorting atoms. ") when I used OPLS, this time it was His 65.
So I used -his optio
On 4/30/13 2:59 AM, Nikunj Maheshwari wrote:
Dear all,
I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o
output.gro)
I used 13. GROMOS 53a6 force field
"Fatal error:
Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while
sorting atoms.
For a hydrogen, th
Dear all,
I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o
output.gro)
I used 13. GROMOS 53a6 force field
"Fatal error:
Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while
sorting atoms.
For a hydrogen, this can be a different protonation state, or it
mi
Hi,
Your problem will likely be solved by not writing the rpath to the
binaries which can be accomplished by setting -DCMAKE_SKIP_RPATH=OFF.
This will mean that you will have to make sure that the library path
is set for mdrun to work.
If that does not fully solve the problem, you might have to b
Dear Gromacs users&devs,
I just installed gromacs-4.5.7 in a Cray XE6m, the serial installation
went fine, however the mpi installation presents a problem. It
compiles fine, but the "make install" (or make install-mdrun) seems to
have problems copying the executable files to the installation
direc
This would normally mean you are somehow calling code from one GROMACS
version with code from another. Some kind of dynamic library loading mishap?
Mark
On Fri, Mar 22, 2013 at 10:41 AM, Nikunj Maheshwari <
nixcrazyfor...@gmail.com> wrote:
> Dear all...
>
> We ran REMD simulations for 36 replica
Dear all...
We ran REMD simulations for 36 replicas. We got an error which stopped the
whole simulation.
"
Reading file md21.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
Reading file md24.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
---
Justin Lemkul
> *To:* Kshatresh Dutta Dubey ; Discussion list for
> GROMACS users
> *Sent:* Tuesday, March 19, 2013 10:48 PM
> *Subject:* Re: [gmx-users] Error during grompp run
>
>
>
> On Tue, Mar 19, 2013 at 10:46 AM, Kshatresh Dutta Dubey <
> kshatr...@ymail.com>
On Tue, Mar 19, 2013 at 10:46 AM, Kshatresh Dutta Dubey wrote:
> Dear Users
>
> I am using groamcs 4.4.4 and when I run grompp during equilibration
> process, it closes with error
> " Fatal error:Topology include file "posre_Protein.itp" not found
> For more information and tips for troubleshoot
Dear Users
I am using groamcs 4.4.4 and when I run grompp during equilibration process, it
closes with error
" Fatal error:Topology include file "posre_Protein.itp" not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentati
That means the automatic download of FFTW did not succeed for some reason.
GROMACS is not going to compile an FFTW for you unless it's sure the FFTW
download was complete and the right file. Either do "make clean" and try
again, or follow the other build instructions to prepare a suitable FFTW
for
Hi, I need install gromacs 4.6.1 in Ubuntu 12.10 when I make the quick and
dirty installation I have this errors:
[ 1%] Performing download step (download, verify and extract) for 'gmxfftw'
-- downloading...
src='http://www.fftw.org/fftw-3.3.2.tar.gz'
dst='/home/biomedicina/gromacs/grom
2006 is prehistoric, for a compiler. See
http://www.gromacs.org/Documentation/Installation_Instructions#3.2._Compiler
Mark
On Wed, Mar 13, 2013 at 7:24 AM, nikunj wrote:
> Hi.
> When I use the "make" command, it always stops at 56% and gives this error:
>
> [ 56%] Building C object
>
> src/gmxl
Dear users
I used gromacs for my system include CNT-water-ion-protein (400,000atom), I
used grompp without error.
after used mdrun with 16 node on cluster, I get this error:
Reading file nvt.tpr, VERSION 4.0.7 (single precision)
Loaded with Money
NOTE: Periodic molecules: can not easily determ
On 03/05/2013 03:50 PM, Mark Abraham wrote:
... and your GROMACS version!
4.6 running on nodes with NVIDIA Keppler K10 and Intel E5 CPU
Mark
On Tue, Mar 5, 2013 at 3:11 PM, Justin Lemkul wrote:
On 3/5/13 4:41 AM, sebastian wrote:
On 03/04/2013 09:47 AM, sebastian wrote:
... and your GROMACS version!
Mark
On Tue, Mar 5, 2013 at 3:11 PM, Justin Lemkul wrote:
>
>
> On 3/5/13 4:41 AM, sebastian wrote:
>
>> On 03/04/2013 09:47 AM, sebastian wrote:
>>
>>> Hi Gromacs user,
>>>
>>> when I try to extend on of my simulations with
>>>
>>> mdrun -deffnm pdz_cis_NVT_disre_
On 3/5/13 4:41 AM, sebastian wrote:
On 03/04/2013 09:47 AM, sebastian wrote:
Hi Gromacs user,
when I try to extend on of my simulations with
mdrun -deffnm pdz_cis_NVT_disre_equi_3 -cpi pdz_cis_NVT_disre_equi_3.cpt
-append
I get the following error
Fatal error:
Count mismatch for state e
On 03/04/2013 09:47 AM, sebastian wrote:
Hi Gromacs user,
when I try to extend on of my simulations with
mdrun -deffnm pdz_cis_NVT_disre_equi_3 -cpi
pdz_cis_NVT_disre_equi_3.cpt -append
I get the following error
Fatal error:
Count mismatch for state entry disre_rm3tav, code count is 0, fi
Hi Gromacs user,
when I try to extend on of my simulations with
mdrun -deffnm pdz_cis_NVT_disre_equi_3 -cpi
pdz_cis_NVT_disre_equi_3.cpt -append
I get the following error
Fatal error:
Count mismatch for state entry disre_rm3tav, code count is 0, file count
is 13
and have no idea whats w
On 3/3/13 6:44 AM, az kalsom wrote:
hi ,
while ruuning the COMMAND
g_energy -f em.edr -o potential.xvg
and following the tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html
i am getting the following error
Select the terms you want from t
On 3/1/13 3:49 PM, Villarealed wrote:
Dear Gromacs-Users,
I am using Gromos96 43a1 FF extended to include phosphorylated residues.
I have a peptide-capped with 17 aminoacids.
When I tried to add ions to the virtual box
I obtained these error
ERROR 1 [file topol.top, line 566]:
No default G9
Dear Gromacs-Users,
I am using Gromos96 43a1 FF extended to include phosphorylated residues.
I have a peptide-capped with 17 aminoacids.
When I tried to add ions to the virtual box
I obtained these error
ERROR 1 [file topol.top, line 566]:
No default G96Angle types
ERROR 2 [file topol.top, line
Hi Stephen,
computing errors from umbrella sampling is not trivial at al.
Generally, there are two possibilities:
- If each histogram overlaps only with one neighboring histogram, you
*must* know the autocorrelation time of each window. This is often a
problem in MD simulations, because there
On 2/26/13 12:51 AM, Anu Chandran wrote:
Sir,
I have tried Berendsen barostat for Pcoupl. Still I get the same error.
So have a look at the other recommendations on the page I linked. Thermostat
instability is just one possibility. We have had numerous reports, just in the
last week, o
Sir,
I have tried Berendsen barostat for Pcoupl. Still I get the same error.
Thank you,
regards,
Anu
On Mon, Feb 25, 2013 at 6:58 PM, Justin Lemkul wrote:
>
>
> On 2/25/13 12:16 AM, Anu Chandran wrote:
>
>> Dear users,
>> I am trying to do a coarse grained simulation of an octamer of a 350
On 2/25/13 12:16 AM, Anu Chandran wrote:
Dear users,
I am trying to do a coarse grained simulation of an octamer of a 350
residue protein in water using gromacs-4.5.3 using martini force field. I
got the following error when i started running NPT equilibration
"Step 32, time 0.64 (ps) LINCS W
Dear users,
I am trying to do a coarse grained simulation of an octamer of a 350
residue protein in water using gromacs-4.5.3 using martini force field. I
got the following error when i started running NPT equilibration
"Step 32, time 0.64 (ps) LINCS WARNING
relative constraint deviation after LI
On 2/19/13 4:53 AM, az kalsom wrote:
hi all,
i generated the ligand topology file by prodrg server and then i generated
the .out file from gaussain software aund used itp adjuster to adjsut the
charges in ligand itp file
but still i am getting the bad box error when i run the editconf command
Dear all,
We have run of three temperatures simulation (unfolding) and three replicates
of them. we are interested to calculate the experimental errors.
anyone has idea how do it?
regards,
Ravi
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx
Hello,
I am writing just to tell how the problem was solved.
I contact a person that works with the BlueGene cluster and he installed
the Gromacs 4.6 in the cluster.
And all my problems were solved. I did not get the same error over and
over again.
Apparently, it was some problem with the 4.
On 2/12/13 5:24 PM, Sonia Aguilera wrote:
Hi,
I was performing a NPT calculation, and I got this error:
The Y-size of the box (6.002812) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (6) times the smallest allowed cell
size (1.000605)
I also tried to chang
Hi,
I was performing a NPT calculation, and I got this error:
The Y-size of the box (6.002812) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (6) times the smallest allowed cell
size (1.000605)
I also tried to change the number of processors but I got the same
On 2/12/13 10:29 AM, vidhya sankar wrote:
Dear Justin Thank you for your reply,
I have set the Restraint Along the Z Axis . as follows
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
i funct fcxfcyfcz
1
Dear Justin Thank you for your reply,
I have set the Restraint Along the Z Axis . as follows
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
i funct fcx fcy fcz
1 1 0 0 100
#endif
A
On 2/6/13 11:52 AM, Bharath K. Srikanth wrote:
Hi everyone,
Today, I was attempting a simulation of a system with a lipid bilayer, and
the size of my simulation box, obtained from a previous simulation, was 15
nm x 7.5 nm x 7.5 nm (15 nm being the direction perpendicular to the plane
of the bi
Hi everyone,
Today, I was attempting a simulation of a system with a lipid bilayer, and
the size of my simulation box, obtained from a previous simulation, was 15
nm x 7.5 nm x 7.5 nm (15 nm being the direction perpendicular to the plane
of the bilayer). The bilayer consisted of 128 DOPC lipids an
On 2/5/13 9:04 AM, Arunima Shilpi wrote:
Dear Sir/ Madam
I am using gromacs for simulation and has the following while running the command for
"grompp"
Expected integer argument for option -maxwarn "".
I do not want use maxwarn to bypass the error.
I request you to kindly help me out to deb
Mark,
Thank you for your answer.
I have already tried to run with several numbers of processors from 8 to
512 and I always got the same error.
And I transfer the simulation to the BlueGene in two different ways. In
both ways, I got the same error.
They were the following:
1) only using the
Dear Sir/ Madam
I am using gromacs for simulation and has the following while running the
command for "grompp"
Expected integer argument for option -maxwarn "".
I do not want use maxwarn to bypass the error.
I request you to kindly help me out to debug the error.
Regards
Arunima
--
gmx-users
On Mon, Feb 4, 2013 at 5:18 PM, Cintia C. Vequi-Suplicy wrote:
>
>
>
> Hello David,
>
> I think it is the pressure.
>
I would think the mentions of pressure are just one of the symptoms. See
http://www.gromacs.org/Documentation/Terminology/Blowing_Up.
You seem to have somewhat more than 100K ato
Hello David,
I think it is the pressure.
Because the error starts with the message below.
But this only happens in the BlueGene cluster. In my local cluster it is
running fine for 60 ns.
Thank you,
Cintia
vol 0.71 imb F 1% vol 0.74 imb F 1% vol 0.73 imb F 1% vol 0.75
imb F 1% vol 0.7
Hello Cíntia,
On 02/01/2013 04:19 PM, Cintia C. Vequi-Suplicy wrote:
Hello Ricardo,
I tried to decrease the integration time but I got the same error.
The system is running fine in my local core.
I have two questions:
1) What do you mean by "I balance the domain decomposition for the
la
Hello Ricardo,
I tried to decrease the integration time but I got the same error.
The system is running fine in my local core.
I have two questions:
1) What do you mean by "I balance the domain decomposition for the
larger number of core"?
2) Are you running simulations at Bluegene P at Rice
On 2013-01-30 23:48, Ricardo Soares wrote:
Hello,
before submitting to Bluegene, I always test the system in my local 8 core
cpu, and if it works, it will also work in Bluegene, as long as I balance the
domain decomposition for the larger number of cores. If your system insists in
exploding, eve
Hello,
before submitting to Bluegene, I always test the system in my local 8 core
cpu, and if it works, it will also work in Bluegene, as long as I balance the
domain decomposition for the larger number of cores. If your system insists in
exploding, even after energy minimization, you could try to
Mark,
Thank you for your answer.
I did an energy minimization with the file em.mdp (below) and then I did
a 40 ns simulation with the same md.mdp I send before. These two steps
were done in my local cluster.
After that I took the configuration for the simulation in the bluegene
and I got th
Hello,
I am having some problems to run my system in a bluegene cluster.
I am running a bilayer simulation. The simulation runs very well in my
local cluster.
After 50ns of simulation on my local cluster with 8 nodes, I got the
configurations and tried to run it in a bluegene with 512 nodes.
On 1/29/13 11:01 AM, az kalsom wrote:
hi,
i am using the following
comamnd
pdb2gmx -ff amber99sb -f proteinamber.pdb -o protei2.pdb -p protein.top
-water spce -ignh
and gets the error
Fatal error:
Residue 2 named GLU of a molecule in the input file was mapped
to an entry in the topology
hi,
i am using the following
comamnd
pdb2gmx -ff amber99sb -f proteinamber.pdb -o protei2.pdb -p protein.top
-water spce -ignh
and gets the error
Fatal error:
Residue 2 named GLU of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entr
On 1/28/13 10:29 AM, Kieu Thu Nguyen wrote:
I reduced time step in equi.mdp file to 20 ps. But the system is still not
balance. Should i continue reduce time step below 20 ps value ? Thanks so
much for any suggestion about appropriate time step value !
The first step I would take is to keep
I reduced time step in equi.mdp file to 20 ps. But the system is still not
balance. Should i continue reduce time step below 20 ps value ? Thanks so
much for any suggestion about appropriate time step value !
Regards,
KT
On Mon, Jan 28, 2013 at 12:53 PM, Kieu Thu Nguyen wrote:
> Thank Justin an
Thank Justin and Tsjerk so much for your help !
I will try smaller time step. And i hope it work :-)
Regards,
KT
On Mon, Jan 28, 2013 at 10:19 AM, Tsjerk Wassenaar wrote:
> Well, 20-30 fs is fine with Martini. But you may have to take care
> initially, and start with a smaller time step.
>
> Ch
Well, 20-30 fs is fine with Martini. But you may have to take care
initially, and start with a smaller time step.
Cheers,
Tsjerk
On Mon, Jan 28, 2013 at 3:11 AM, Justin Lemkul wrote:
>
>
> On 1/27/13 12:15 PM, Kieu Thu Nguyen wrote:
>
>> @Justin,
>> Fmax=8.0226669e+00
>>
>
> OK, that looks goo
On 1/27/13 12:15 PM, Kieu Thu Nguyen wrote:
@Justin,
Fmax=8.0226669e+00
OK, that looks good.
the system includes protein, lipid, water, ion Cl-
em.mdp file is
integrator = steep
tinit= 0.0
dt = 0.02
nsteps = 5
n
@Justin,
Fmax=8.0226669e+00
the system includes protein, lipid, water, ion Cl-
em.mdp file is
integrator = steep
tinit= 0.0
dt = 0.02
nsteps = 5
nstcomm = 1
nstxout = 5000
nstvout
1 - 100 of 1054 matches
Mail list logo
