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
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
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
P
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
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
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:
>
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
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
Please do not reply to the entire digest. It gets hopelessly confusing.
On 6/24/13 10:51 AM, Raji Viswanathan wrote:
I am using Red Hat Enterprise Linux 5.5
Raji
Something about your shell environment is probably hosed. Do other commands
that prompt for interactive input work, or just geni
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
On 1/26/13 8:17 PM, Kieu Thu Nguyen wrote:
Thank Tsjerk so much !
But after being minimized 5 steps and equilibrated 90 ns, there are
some bonds in the system that rotate more than 30 degrees.
I applied tips for blew up system as you advised. But the system does not
achieve balance.
Should
Thank Tsjerk so much !
But after being minimized 5 steps and equilibrated 90 ns, there are
some bonds in the system that rotate more than 30 degrees.
I applied tips for blew up system as you advised. But the system does not
achieve balance.
Should i carry out more many steps for minimization ?
Hi KT,
This is caused by another problem. Your system blew up. Check messages
before this one, and check the log for LINCS warnings.
Cheers,
Tsjerk
On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen wrote:
> Dear All,
>
> My MD simulation has an error
>
> Warning: Only triclinic boxes with the
On 1/4/13 5:06 AM, Kieu Thu Nguyen wrote:
Thank Neha ! I follow your advices but this error still appear. I don't
know why.
You'll have to show us exactly what you're doing to get any solid advice.
Consider what I posted earlier. Usually the mismatch occurs because you are
using a coordin
On 1/4/13 12:51 AM, Kieu Thu Nguyen wrote:
Dear All,
When using the command
grompp -f equi.mdp -c membedded.gro -p merged.top -n index.ndx -o
equilibrate.tpr
The error is
Fatal error:
Invalid atom number 6518 in indexfile
How can i fix this ?
Hard to say. You haven't told us what's in the s
Thank Neha ! I follow your advices but this error still appear. I don't
know why.
By the way, does anybody know why there are not ions in topology file in
Martini CG-MD. Because I see the system has not zero charge, i don't
understand why the CG system not be neutralized by ions.
Thanks and regar
First check your .gro file and your .top file, to make sure atom 6518 (or
Water) is consistently defined.
Next step would be to make sure this atom features in the index file within a
"correct group".
In some cases, if a single atom is left out and not part of any group in the
index file, it gives
On 12/17/12 8:47 PM, Christopher Samuel wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On 17/12/12 21:57, ananyachatterjee wrote:
[ganga:04205] *** Process received signal *** [ganga:04205] Signal:
Segmentation fault (11) [ganga:04205] Signal code: Address not
mapped (1) [ganga:04205]
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On 17/12/12 21:57, ananyachatterjee wrote:
> [ganga:04205] *** Process received signal *** [ganga:04205] Signal:
> Segmentation fault (11) [ganga:04205] Signal code: Address not
> mapped (1) [ganga:04205] Failing at address: 0x201a01c20
Segmentation
Thank Justin !
On Tue, Dec 18, 2012 at 7:20 AM, Justin Lemkul wrote:
>
>
> On 12/17/12 7:17 PM, Kieu Thu Nguyen wrote:
>
>> Dear All,
>>
>> When i do step EM, the output file .gro is separated into many step.pdb
>> files . And many errors "Water molecule starting at atom XXX can not be
>> sett
On 12/17/12 7:17 PM, Kieu Thu Nguyen wrote:
Dear All,
When i do step EM, the output file .gro is separated into many step.pdb
files . And many errors "Water molecule starting at atom XXX can not be
settled" appears. And the potential energy is positive !
What should i do to solve it ?
Pl
I have just found the right group is 15 (SOL) :-)
Thanks so much and sorry about my stupid question !
On Mon, Dec 17, 2012 at 11:40 PM, Justin Lemkul wrote:
>
>
> On 12/17/12 11:38 AM, Kieu Thu Nguyen wrote:
>
>> Thank Justin ! I found my mistake. But when i type the next command line
>>
>>
On 12/17/12 11:38 AM, Kieu Thu Nguyen wrote:
Thank Justin ! I found my mistake. But when i type the next command line
genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname
CL -nn 4
and choose group 0 (system), the error is
Fatal error:
No line with moleculetype 'System'
Thank Justin ! I found my mistake. But when i type the next command line
genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname
CL -nn 4
and choose group 0 (system), the error is
Fatal error:
No line with moleculetype 'System' found the [ molecules ] section of file
'topol.top
On 12/17/12 9:24 AM, Kieu Thu Nguyen wrote:
Dear All,
When i do the "Step Four: Adding Ions"in the tutorial "KALP-15 in DPPC", it
appears the error:
Fatal error:
No such moleculetype W
I checked .top file and included.itp files, they have definded water
molecule type name is "W".
What happe
On 12/17/12 9:14 AM, Kieu Thu Nguyen wrote:
Dear Justin,
The nvt.mdp file is:
define= -DPOSRES; position restrain the protein
; Run parameters
integrator= md; leap-frog integrator
nsteps= 5; 2 * 5 = 100 ps
dt= 0.002; 2 fs
; Outpu
Dear Justin,
The nvt.mdp file is:
define= -DPOSRES; position restrain the protein
; Run parameters
integrator= md; leap-frog integrator
nsteps= 5; 2 * 5 = 100 ps
dt= 0.002; 2 fs
; Output control
nstxout= 100; save coo
On 12/17/12 8:53 AM, Kieu Thu Nguyen wrote:
Dear All,
I'm practising the tutorial 2a (protein in water) in the MARTINI tutorial.
After doing step 6 (Do a short energy minimization and position restrained
simulation),i carry out running NVT equilibrium. But it appears the error
in the terminal
On 12/17/12 5:57 AM, ananyachatterjee wrote:
Dear all,
While running mdrun using following mdpparameters:
title= Model MD
; Run parameters
integrator= md
nsteps= 500
dt= 0.002
; Output control
nstxout= 500
nstvout= 500
nstxtcout= 500
nstene
I have not followed the thread but concerning the solvation of a
protein using genbox you need to:
1- use a box of water that has the exact size of the final box you
want (you make it yourself using any tool you want) and you need to
define the box size of the protein file as the one of the
Tanks to all for your advices,
I am going to check all the different aspect you suggested and I will
report the results as soon as possible.
Francesco
2012/12/11 Tsjerk Wassenaar
> Hi,
>
> Visualization is the key. If you check the structure right after genbox,
> you should be able to notice s
Hi,
Visualization is the key. If you check the structure right after genbox,
you should be able to notice something odd. Apparently genbox has a problem
with martini water, which probably means there is a problem with monoatomic
solvents. The problem has been noted before, b ut I'm a bit too lazy
On Mon, Dec 10, 2012 at 11:54 PM, Justin Lemkul wrote:
>
>
> On 12/10/12 5:45 PM, francesco oteri wrote:
>
>> For Justin,
>> I need this water for one simple reason: less then 20nm doesn't workAs
>> I said before
>>
>>
> It seems you have identified the source of the problem, and it is
> inde
On Mon, Dec 10, 2012 at 11:44 PM, francesco oteri wrote:
> Hi Mark,
> you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to
> use 0.21. Since I still got errors with this procedure, I decided to remove
> water manually through vmd.
>
Don't change things until you know *why* t
On 12/10/12 5:45 PM, francesco oteri wrote:
For Justin,
I need this water for one simple reason: less then 20nm doesn't workAs
I said before
It seems you have identified the source of the problem, and it is independent of
box size. I questioned the box size because it seemed rather ran
For Justin,
I need this water for one simple reason: less then 20nm doesn't workAs
I said before
2012/12/10 francesco oteri
> Hi Mark,
> you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to
> use 0.21. Since I still got errors with this procedure, I decided to remove
>
Hi Mark,
you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to
use 0.21. Since I still got errors with this procedure, I decided to remove
water manually through vmd.
Looking carefully at the configurations, I found that the water molecule
originating the error is exactly super
On Mon, Dec 10, 2012 at 11:15 PM, francesco oteri wrote:
> Actually, since I copied and pasted the mail, there is an imprecision. When
> I use 20nm as box side lenght I don't get
> any error, everything goes fine.
>
> I actually tested different size between 19 and 20 nm and I found that the
> mi
On 12/10/12 5:15 PM, francesco oteri wrote:
Actually, since I copied and pasted the mail, there is an imprecision. When
I use 20nm as box side lenght I don't get
any error, everything goes fine.
I actually tested different size between 19 and 20 nm and I found that the
minimum size to avoid th
Actually, since I copied and pasted the mail, there is an imprecision. When
I use 20nm as box side lenght I don't get
any error, everything goes fine.
I actually tested different size between 19 and 20 nm and I found that the
minimum size to avoid the error is 19.5nm.
My system has an average size
On Mon, Dec 10, 2012 at 9:48 PM, francesco oteri
wrote:
> Dear gromacs users,
>
> I am facing a very tricky problem in building a stable topology.
> In particular I am trying to use MARTINI force-field and I noticed that if
> I use a box whose the side size is smaller than 20nm, the minimization
>
On 12/10/12 3:48 PM, francesco oteri wrote:
Dear gromacs users,
I am facing a very tricky problem in building a stable topology.
In particular I am trying to use MARTINI force-field and I noticed that if
I use a box whose the side size is smaller than 20nm, the minimization
fails with this mes
Hard to say. Your compiler is prehistoric, and things to do with pthreads
are the province of the compiler, so getting a more recent version will
probably fix it.
Mark
On Mon, Dec 10, 2012 at 7:32 AM, BHARATI DUTTA wrote:
> Hi,
>
> The following error pops up during compilation of Gromacs-4.5.5
On 11/29/12 7:49 AM, Shine A wrote:
Sir,
I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
Now doing nvt equilibration.During mdrun (mdrun -deffnm nvt) getting error
like this
Fatal error:
6 particles communicated to PME node 1 are more than 2/3 times the cut-off
ou
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