are running fine.
further, $mdrun_mpi just results in a blinking cursor at newline
(earlier it displayed an array of info strings)
> Mark
-Manik
>
> - Original Message -----
> From: Manik Mayur
> Date: Saturday, August 14, 2010 15:14
> Subject: [gmx-users] Parallel mdrun not wo
b6d6f000)
/lib/ld-linux.so.2 (0xb77f7000)
Please somebody tell me what is the problem?
Thanks,
Manik Mayur
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
-
g_potential -f Soln.trr -s Sim_ions.tpr -n Soln.ndx -o potential.xvg -oc
charge.xvg -d Z
Selected 4: 'Ions'
trn version: GMX_trn_file (single precision)
Reading frame 0 time 1000.000
Dividing the box in 10 slices
Segmentation fault
Thanks,
Manik Mayur
Graduate student
Microfluidics La
to resemble a
> nail.
>
>
>
> *From:* gmx-users-boun...@gromacs.org [mailto:
> gmx-users-boun...@gromacs.org] *On Behalf Of *Manik Mayur
> *Sent:* Friday, 20 November 2009 2:10 AM
> *To:* Discussion list for GROMACS users
> *Subject:* [gmx-users] Hydrated radius of ion
Hi,
Is there any gromacs utility to calculate the hydrated radius of ions?
Thanks,
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search
2009/11/17 Nilesh Dhumal
> this is the command,
>
> pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter
>
> Here I have attached the dioxin.pdb file.
>
Check your dioxing.pdb.. there might be formatting issues. It might happen
the due to bad format of the pdb file, your 'L' is somehow removed from
'C
2009/9/29 Justin A. Lemkul
>
>
> Carla Jamous wrote:
>
>>
>> Thank you for your reply,
>> but none of the water molecules with error messages is trapped inside my
>> protein, nor is it in contact with the protein or the ions in my system.
>>
>>
Also if the water molecules are positioned properly,
rchive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
Manik Mayur
Grad
LinkedIn
Manik Mayur requested to add you as a connection on LinkedIn:
--
Chinmay,
I'd like to add you to my professional network on LinkedIn.
- Manik
Accept invitation from Manik Mayur
http://www.linkedin.
use editconf -f file.pdb -o file.gro
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
2009/9/10 Amit Choubey
> hi everyone,
> I have a pdb file of my system and i want it to be fed into the GROMACS
> software. I have a new force fiel
= 173529
>>
>> ; OPTIONS FOR BONDS
>> constraints = none
>> ; Type of constraint algorithm
>> constraint-algorithm = Lincs
>> ; Do not constrain the start configuration
>> continuation = no
>> ; Use successive overr
with?
Thanks,
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http
^(1/6)).
With regards,
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
On Thu, Jul 30, 2009 at 5:56 PM, Vitaly V. Chaban wrote:
> If you unzipped/untarred the archive properly it should be some system
> already prepared to run. So you can just s
y at x=a doesn't vary much
with the #bins.
If you have faced the same problem, how do you resolve it?
Thanks and regards,
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
___
gmx-users mailing listgmx-u
On Mon, Jun 29, 2009 at 1:51 PM, Mark Abraham wrote:
> Manik Mayur wrote:
>
>> Hi,
>> I am trying to install GROMACS-4.0.5, but while making mpirun with the
>> option --enable-mpi it gives the following sets of errors:
>>
>> ../gromacs-4.0.5/src/gmxlib/.libs/l
On Mon, Jun 29, 2009 at 12:54 PM, Manik Mayur wrote:
> Hi,
> I am trying to install GROMACS-4.0.5, but while making mpirun with the
> option --enable-mpi it gives the following sets of errors:
>
read "making mdrun"
../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so:
The important thing to note is that I have successfully compiled and
installed mpi version of mdrun on the same machine, for GROMACS-4.0.4.
What am I missing here?
Thanks,
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
_
mx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> Florian Dommert
> Dipl.-Phys.
>
> Institute for Computational Physics
> University Stuttgart
>
> Pfaffenwaldring 27
> 70569 Stuttgart
&
On Fri, Jun 12, 2009 at 8:46 AM, Mark Abraham wrote:
> Manik Mayur wrote:
>
>> Hi,
>>
>> The last mail supposedly bounced from the server due to attachments. So
>> please excuse in case you find this as a repetition.
>>
>> I am trying to simula
at address: (nil)
[md-comp1:32377] [ 0] [0xb7fd8440]
[md-comp1:32374] [ 0] [0xb7ef0440]
[md-comp1:32374] *** End of error message ***
[md-comp1:32377] *** End of error message ***
I would be extremely thankful, if somebody points me to the source of the
error and the workaround.
Thanks,
Manik Mayu
On Fri, Jun 5, 2009 at 11:58 PM, Jussi Lehtola wrote:
> On Fri, 2009-06-05 at 23:28 +0530, Manik Mayur wrote:
> > Hi,
> > I am trying to equilibrate a box of SPC/E water using NVT simulations.
> > After 2 ns of equilibration my pressure is still <0 bars. Is it an
>
ite time of equilibration? Can anyone point me to fundamental theory
pertaining to this behavior as I couldn't find any upon googling.
Please do not suggest doing NPT as for some reason I want to avoid it for
now.
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT K
ch before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechani
; > Regard
> > Rituraj
> >
> >
> >
> > --
> > "The future belongs to those who believe in the beauty of their dreams."
> >
> >
> > --
> >
> > Message: 8
> > Date: Thu, 04 Jun 2009
On Wed, Jun 3, 2009 at 9:04 PM, Justin A. Lemkul wrote:
>
>
> Manik Mayur wrote:
>
>> Hi,
>>
>> Even though after going through the manual, I still have some basic
>> confusions regarding generating topologies.
>>
>> 1) I have generated an itp fil
) I am using GROMOS96 43a1, so am I allowed to change combination rule to
'2' ( '1' is the default). How significantly will it affect the
simulations?
Any relevant idea/suggestion/reference is appreciated.
Thanks,
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of
http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gro
On Thu, May 14, 2009 at 1:56 AM, Justin A. Lemkul wrote:
>
>
> Manik Mayur wrote:
>
>> On Thu, May 14, 2009 at 1:32 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Manik Mayur wrote:
>>
>>Hi Users,
>>
&g
On Thu, May 14, 2009 at 1:32 AM, Justin A. Lemkul wrote:
>
>
> Manik Mayur wrote:
>
>> Hi Users,
>>
>> I constructed a .pdb file for TIP4P water model which I tried to convert
>> to .gro using pdb2gmx using:
>>
>> $ pdb2gmx -f Sim1.pdb -o Sim1.
W3? How is the OW-HW3
bond is getting stretched? Also, what should be the correct procedure for
the conversion?
Thanks,
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
___
gmx-users mailing listgmx-users@g
On Fri, Apr 3, 2009 at 11:11 PM, David van der Spoel
wrote:
> Manik Mayur wrote:
>
>>
>>
>> On Fri, Apr 3, 2009 at 10:47 PM, David van der Spoel <
>> sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>> wrote:
>>
>>Manik Mayur wrote:
>&g
On Fri, Apr 3, 2009 at 10:47 PM, David van der Spoel
wrote:
> Manik Mayur wrote:
>
>>
>>
>> On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel
>> > sp...@xray.bmc.uu.se>> wrote:
>>
>>Manik Mayur wrote:
>>
>>
&
On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel wrote:
> Manik Mayur wrote:
>
>>
>>
>> On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel
>> > sp...@xray.bmc.uu.se>> wrote:
>>
>>Manik Mayur wrote:
>>
>>Hi,
>>
On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel wrote:
> Manik Mayur wrote:
>
>> Hi,
>>
>> With reference to
>>
>> http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html
>>
>> I would like to know if anybody has successfully simul
giving constant
velocity to a group of atoms, as we can do in LAMMPS, in future versions.
It will really be a life saver if GROMACS can be used for such problems.
Also can we build GROMACS as a library to be called from customized codes?
Thanks,
--
Manik Mayur
Graduate student
Microfluidics Lab
Dept
o gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
___
gmx-users mailing listgmx-users@gromacs.org
ease don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
II
On Tue, Mar 17, 2009 at 9:31 PM, Manik Mayur wrote:
>
>
> 2009/3/17 Berk Hess
>
>> Hi,
>>
>> You pull rate is ridiculously high (1 nm/ps).
>>
>
Also I am simulating in reduced dimentions. I think it is fine then.
Is there any upper limit on the pu
vec[0]= 1.0e+00
> vec[1]= 0.0e+00
> vec[2]= 0.0e+00
> init (3):
> init[0]= 2.08088e+00
> init[1]= 0.0e+00
> init[2]= 0.0e+00
> rate = 1
> k= 0
> kB
00
rate = 1
k= 0
kB = 0
The other useful data might be:
OS- Ubuntu 8.04
Gromacs- 4.0.2
Thanks,
Manik Mayur
--
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
md.log
Description: Binary data
eql.mdp
On Wed, Mar 4, 2009 at 2:25 AM, Mark Abraham wrote:
> Manik Mayur wrote:
>
>>
>>
>> On Wed, Mar 4, 2009 at 1:55 AM, Roland Schulz > rol...@utk.edu>> wrote:
>>
>>You will have to recompile everything:
>>make clean
>>make
>
, as for now, its working to my need.
But somehow still I feel that with openmpi-1.3, gromacs-4.0.4 and Xeon Quad
core at 3.6Ghz, the processing speed which I am getting, is quite low.
You still have references to lam in your libmd_mpi.so
>
> Roland
>
> On Tue, Mar 3, 2009 at 3:0
On Wed, Mar 4, 2009 at 1:18 AM, Roland Schulz wrote:
> you will have to set
>
> LD_LIBRARY_PATH to /home/openmpi/lib
>
I have tried that.. the error still persists.
use either setenv or export depending on your shell
>
> Roland
>
> On Tue, Mar 3, 2009 at 2:35 PM, Manik
to `kpause'
../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_next'
../mdlib/.libs/libmd_mpi.so: undefined reference to `rev8'
../mdlib/.libs/libmd_mpi.so: undefined reference to `argvadd'
../mdlib/.libs/libmd_mpi.so: undefined reference to `bfiselect'
../mdlib/.libs/libmd_m
On Wed, Mar 4, 2009 at 12:28 AM, Nicolas wrote:
> Manik Mayur a écrit :
>
>>
>>
>> On Tue, Mar 3, 2009 at 11:47 PM, Nicolas > nsa...@ucalgary.ca>> wrote:
>>
>>Manik Mayur a écrit :
>>
>>Hi,
>>
>>If I
On Tue, Mar 3, 2009 at 11:47 PM, Nicolas wrote:
> Manik Mayur a écrit :
>
>> Hi,
>>
>> If I have 2 mpi environments, namely LAM and openMPI, and I want gromacs
>> to use openMPI of the two, what extra option should I pass during the
>> ./configure step? In my
run mdargs
> lamhalt
>
> I don't use Lam often, though, you might need to use different Lam options.
>
> Nicolas
>
> Manik Mayur a écrit :
>
>> Hi,
>>
>> I have till now successfully used openMPI and gromacs together. Recently I
>> got a cluste
Hi,
I have till now successfully used openMPI and gromacs together. Recently I
got a cluster where I tried to install openMPI and gromacs locally as I
donot have root priviledges on it. But it turns out that it already has MPI
environment on it (LAM) which I donot want to use (as the version is qu
On Tue, Feb 24, 2009 at 9:44 PM, Justin A. Lemkul wrote:
>
> Hi,
>
> I have a quick question about interpreting the output from g_hbond. I am
> using the -ac option to calculate H-bond lifetimes between my protein and a
> series of different, bound ligands. I read the associated paper, but I
>
quests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-Manik Mayur
--
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
___
On Fri, Feb 20, 2009 at 2:45 PM, nitu sharma wrote:
> Dear All,
>
> I have successfully insstalled gromacs on my 32 bit
> i686 linux system but when I give the mdrun command for running gromacs on
> my system the output is like this
>
> "mdrun: error while loading shared lib
On Thu, Feb 19, 2009 at 10:45 AM, nitu sharma wrote:
> *Dear All,
>
> I have compiled fft-3.2.1 in a specific user directory; then configured,
> compiled gromacs-4.0.3 from source code according to directions and installed
> it in the
> specific directory, all without any errors, but at the end "
On Sat, Dec 27, 2008 at 6:36 PM, Justin A. Lemkul wrote:
> Quoting Manik Mayur :
>
> > On Sat, Dec 27, 2008 at 3:12 PM, Manik Mayur
> wrote:
> >
> > > Hi all,
> > >
> > > I have a few probIems/confusions and will be extremely thankful for any
On Sat, Dec 27, 2008 at 3:12 PM, Manik Mayur wrote:
> Hi all,
>
> I have a few probIems/confusions and will be extremely thankful for any
> help. I added some "Cl- ions" by replacing water using "genion (and -nn)".
> It generated a "topol.top" fil
Hi all,
I have a few probIems/confusions and will be extremely thankful for any
help. I added some "Cl- ions" by replacing water using "genion (and -nn)".
It generated a "topol.top" file with Cl listed in [ molecules ]. Now when I
try to run grompp, it gives an error saying "no such molecule type
Hi,
I have a system (a slit type nanopore) in which I have 4 wall layers. I
would like to distribute partial charges on the first wall layer (the layer
in contact with the fluid). The wall layers are made of Si atoms. I tried to
change ffG43a1nb.itp (& ffG43a1.atp) by adding a new atom with
charac
On Sun, Dec 21, 2008 at 5:04 PM, Chitrita Dutta Roy
wrote:
> Thanks to all for helping me previously.
> Now i am unable to arrange the .tpr file for position restraint mdrun on a
> quad core as in version 4.0.2 grompp -np is not a valid comand can anybody
> help me in building a tpr file for paral
I am not sure that mdrun_mpi or for that matter mdrun with options -np 2
-multi 1 (I have a core 2 duo machine) is actually running the process
parallely, as the estimated time for completion for a simulation is the same
as without.
I have built open-mpi library, so do I have to make some changes
cussion list for GROMACS users
> Message-ID: <49418d58.9010...@anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Manik Mayur wrote:
> > Hi,
> > I am trying to remove thermostat on a certain group of atoms by taking
> > tau_t = 0. B
Hi,
I was wondering if there is any way to:
1) COMM removal in a specific dimension just life freezedim. e.g. I want
COMM removal in y-direction only.
2) Get WCA potential by setting [vdw-type: Shift] and [rvdw=2^(1/6)*sigma];
As in WCA the repulsive part of LJ is retained by setting the cutoff rad
Hi,
I am trying to remove thermostat on a certain group of atoms by taking tau_t
= 0. But upon using grompp it says:
"For proper thermostat integration tau_t (0) should be more than an order of
magnitude larger than delta_t."
And gives a warning. This was not there in v3.3. Is this a bug or shoul
size of COMM removal and Tau_t of the thermostat?
Thanks,
Manik Mayur
--
_
HAPAX LEGOMENA
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http
Hi,
I have developed a co-ordinate file for Argon atoms bounded by wall atoms
with properties same as Argon. When I am doing the energy minimization, it
shows a max. force equal to inf. on a certain atom. This is for the case
when I am using "simple" in the neighbour search, when I use "grid" it gi
63 matches
Mail list logo
