[gmx-users] pdb2gmx segmentation fault

Hi, I have installed the latest version of gromacs 4.5.4 and the installation went fine. When I run pdb2gmx I get Segmentation fault even before I could select the force field options. I tried with different pdb files and I get seg fault without any other error messages. The command is: pdb2gmx -f

Re: [gmx-users] pdb2gmx segmentation fault

appreciated. Thanks and Regards, Raghu Subject: Re: [gmx-users] pdb2gmx segmentation fault To: Discussion list for GROMACS users Message-ID: <4dae452b.3090...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/20/2011 7:38 AM, Ragothaman Yennamalli wrote: > Hi,

Re: [gmx-users] pdb2gmx segmentation fault

me problem with pdb2gmx. Hence installed the latest version. Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 7:39 AM, Justin A. Lemkul wrote: > > > Ragothaman Yennamalli wrote: > >> I had the issue of shared libraries while installing which I did >> troubleshoot and the in

Re: [gmx-users] pdb2gmx segmentation fault

t think it is the issue since I have used the flag --enable-shared. Also, if this was the case then editconf would not have worked as well. Thanks and Regards, Raghu On Wed, Apr 20, 2011 at 8:33 AM, Justin A. Lemkul wrote: > > > Ragothaman Yennamalli wrote: > >> These wer

Re: [gmx-users] pdb2gmx segmentation fault

On Wed, Apr 20, 2011 at 9:46 AM, Justin A. Lemkul wrote: > > > Ragothaman Yennamalli wrote: > >> Dear Justin, >> >> Thanks for the mail. Yes, without these CFLAGS the "make" was not >> successful. Yes I did set the CPPFLAGS and LDFLAGS before con

Re: [gmx-users] pdb2gmx segmentation fault

It is a SunOS operating system, 64 bit with Eight 6-core AMD opteron CPUs. On Wed, Apr 20, 2011 at 11:34 AM, Matthew Zwier wrote: > I've never seen the -D_POSIX_PTHREAD_SEMANTICS before. What caused > you to need to define that flag? > > Also...what hardware (cpu) and operating system (linux? w

Re: [gmx-users] pdb2gmx segmentation fault

Hi all, With the help of my colleague Nathan Weeks I am able to run pdb2gmx and all other commands successfully . Here are his responses which he wanted me to share with you in case someone is trying to install Gromacs in a similar system. We set CFLAGS that way due to the following message when r

Re: [gmx-users] pdb2gmx segmentation fault

Thanks for the link. Have just filed it. Thanks and Regards, Raghu On Fri, Apr 22, 2011 at 1:12 PM, Justin A. Lemkul wrote: > Matthew Zwier wrote: > >> Nice catch on the readdir_r(). I wonder if the developers would >> appreciate a bug report and patch for your fix. >> >> > Yes, please file an

[gmx-users] free energy calculations

Hi, I want to run free energy calculations on a particular protein-ligand complex. I do not have much knowledge on this so I have some questions, hopefully someone might give me clear answers. I am following the tutorial given in this link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/g

[gmx-users] Re: free energy calculations

> > > Message: 1 > Date: Tue, 05 Jul 2011 19:14:04 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] free energy calculations > To: Discussion list for GROMACS users > Message-ID: <4e139abc.1030...@vt.edu> > Content-Type: text/plain; charset=I

Re: [gmx-users] free energy

Please see this... http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html Raghu On Sun, Jul 10, 2011 at 12:33 PM, balaji nagarajan wrote: > Dear Users ! > > Is it possible to calculate the free energy for a molecule , > > at the zero step MD , when i see t

[gmx-users] where is water?

Hi Friends, When I run pdb2gmx, it automatically asks which water topology should be included. Also, in the .top file the lines included are: ; Include water topology #include "gromos53a6.ff/spc.itp" However, I do not see any water molecules in the .gro file. So, was water included or not? Than

Re: [gmx-users] where is water?

Thanks...Glad to realize the newer version of gromacs makes life easier. Raghu On Mon, Jul 11, 2011 at 11:38 AM, Justin A. Lemkul wrote: > > > Ragothaman Yennamalli wrote: > >> Hi Friends, >> >> When I run pdb2gmx, it automatically asks which water topology shoul

Re: [gmx-users] simulation of oligomers/monomers

Look at this paper where the simulation was done on a protein dimer: http://www.ncbi.nlm.nih.gov/pubmed/17027497 On Mon, Jul 18, 2011 at 2:50 AM, Mark Abraham wrote: > On 18/07/2011 3:08 PM, Kavyashree M wrote: > >> Dear users, >> >> I am working on a protein which is a dimer (in the crystal stru

Re: [gmx-users] simulation of oligomers/monomers

is a part of a bifunctional protein which is an octamer. So > Because of all these > confusions I through some information could be obtained from a monomeric > simulation.. > Is it reasonable? > > > Thanking you > With Regards > M. Kavyashree > > On Mon, Jul 18, 201

[gmx-users] protein ligand

Hi, I know this is off topic. Can someone please suggest independent scoring functions that can calculate binding energies between protein and ligand? Thanks and Regards, Ragothaman -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please sear

[gmx-users] running at higher temperatures

Hi, When running simulations at a constant higher temperatures (such as simulating a thermophile) would changing "ref_t" and "gen_temp" to the appropriate kelvin is enough? Thanks and Regards, Raghu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] Trajectory viewing by freeing a part

Hi, While viewing a trajectory I am trying to see how a particular part or group is behaving, while keeping the rest frozen (I dont want them to move). For example, in a two domain protein keeping one domain frozen and seeing the other domain movement or in a protein ligand complex keeing the prote

[gmx-users] error while compiling gromacs 4.0.2

Dear all, While compiling gromacs 4.0.2 in a AMD 64bit dual processor system, I encounter the following error while configuring: checking size of int... configure: error: cannot compute sizeof (int) See `config.log' for more details. Please let me know where I have gone wrong. I am pasting the e

[gmx-users] error while compiling gromacs 4.0.2

Dear all, I tried installing the new version of gromacs. Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] plz ignore my previous mail

Sorry..for sending an incomplete mail. Please ignore my previous mail. Raghu Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman

[gmx-users] Gromacs version

Hi, Can anyone please tell me how to find which version of gromacs is installed in a particular system? Since with the path where it is installed, I am unable to make out if it 3.2.1 or 3.3. Thanks in advance, Raghu Forgot the famous last words? Access your message archive online at ht

Re: [gmx-users] Gromacs version

> Tsjerk > > On Jan 5, 2008 8:38 AM, Ragothaman Yennamalli > <[EMAIL PROTECTED]> wrote: > > > Hi, > > Can anyone please tell me how to find which > version of > > gromacs is installed in a particular system? Since > > with the path where it is ins

[gmx-users] error while running grompp

Dear all, We are trying running Gromacs in different systems with different number of processors. In sun opteron cluster we checked and it ran perectly fine. When, using the same input files, to run in apple g5 system with same number of processors. I get the following message when I run grompp: c

Re: [gmx-users] error while running grompp

<[EMAIL PROTECTED]> wrote: > Ragothaman Yennamalli wrote: > > Dear all, > > We are trying running Gromacs in different systems > > with different number of processors. In sun > opteron > > cluster we checked and it ran perectly fine. When, > > using the sam

[gmx-users] query related to rerunning MD

Hi all, A query related to rerunning MD. For eg: After 5ns run of MD I need to rerun from 3ns and I take the structure closest to it from the trajectory files. Taking this 3ns.gro as the starting structure I redo all the steps for preparation. In such a case, I am assuming that the velocity will b

[gmx-users] query about diferent cutoffs

Dear all, In a particular setup of a protein interacting with ions, the protein needs to be simulated without ions and after a certain point of time the ions are introduced to the system, so as to check of the protein undergoes refolding in the presence ions or not. Since it is a known fact that in

[gmx-users] mpi error

Dear all, I had been running many runs of mdrun in a Sun opteron cluster with each node having 4 processors. When I ran my latest mdrun after 15ns run, I get the following error and mdrun exits without any error message on other log files. *** mp

[gmx-users] trjconv error

I wanted to truncate a trajectory file and when I use trjconv tool, I get an error: Fatal error: /media/usbdisk1/paul_case4/full_10ns_040408/traj2.xtc is not a trj file, exiting The file is able to read by gmxcheck... What could be the problem? Thanks in advance. Regards, Ragothaman Ex

Re: [gmx-users] trjconv error

ark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] trjconv error > To: "Discussion list for GROMACS users" > Date: Friday, 18 April, 2008, 8:09 PM > Ragothaman Yennamalli wrote: > > I wanted to truncate a trajectory file and when I use > > trjconv tool, I ge

Re: [gmx-users] trjconv error

Wed, 23/4/08, Mark Abraham <[EMAIL PROTECTED]> wrote: > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] trjconv error > To: "Gromacs Users" > Date: Wednesday, 23 April, 2008, 11:44 AM > Ragothaman Yennamalli wrote: > > Hi, > > Sor

[gmx-users] Error while running starting grompp and mdrun

Dear all, I get an error while running grompp or mdrun in a Sun cluster. Each node has 4 processors. I am submitting the job via a SGE script. After, I submit the job by "$qsub test_gromacs", the run terminates with the following message in the log file. Please tell me how to troubleshoot this p

Re: [gmx-users] Error while running starting grompp and mdrun

Dear Mark, Thanks for the mail. > > Since there's three different usages of -np you'd > need to be more > precise to make a good description of your problem. > I was changing the -np option in mdrun and grompp. > The symptoms you observe make sense if $NSLOTS==1. Since > all three -np > fla

[gmx-users] removing a water molecule

Dear all, I am running a MD simulation, which stops after 6ns run with an error saying: t = 6825.932 ps: Water molecule starting at atom 19637 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates How does one proceed from here

Re: [gmx-users] removing a water molecule

wrote: > Ragothaman Yennamalli wrote: > > Dear all, > > I am running a MD simulation, which stops after > 6ns > > run with an error saying: > > > > t = 6825.932 ps: Water molecule starting at atom > 19637 > > can not be settled. > > Check for bad con

Re: [gmx-users] removing a water molecule

e sort of part of the protein, but are > coupled to the solvent > outside. One common source for > LINCS/water-molecule-can't-be-settled > errors. > > Cheers, > > Tsjerk > > On 5/28/07, Mark Abraham <[EMAIL PROTECTED]> > wrote: > > Ragothaman Yennamall

Re: [gmx-users] [Fwd: Problem with Position restrained dynamics]

Can you send us the pr.mdp file? Regards, Raghu --- David van der Spoel <[EMAIL PROTECTED]> wrote: > > > Original Message > Subject: Problem with Position restrained dynamics > Date: Tue, 24 Jul 2007 19:19:39 +0530 > From: E BHARATHY <[EMAIL PROTECTED]> >

[gmx-users] LINCS warning

Dear all, I have a query, 1. Are two trajectories comparable if each one of them has been run in a different version of gromacs? Eg, v3.2 and v3.3. Thanks in advance, Regards, Raghu ** Y. M. Ragothaman, Research Scholar, Centre for Computational Biology and Bio

[gmx-users] Gromacs version

Dear all, I have a query, 1. Are two trajectories comparable if each one of them has been run in a different version of gromacs? Eg, v3.2 and v3.3. Thanks in advance, Regards, Raghu ** Y. M. Ragothaman, Research Scholar, Centre for Computational Biology and Bio

[gmx-users] MPIRUN error while running position restrained MD

Dear all, I am running gromacs3.2 version. When I am running the position restraint md for the protein, the process stops within 100 steps with the following error: - One of the processes started by mpirun has exited with

Re: [gmx-users] MPIRUN error while running position restrained MD

TED]> wrote: > Ragothaman Yennamalli wrote: > > Dear all, > > I am running gromacs3.2 version. When I am running > the > > position restraint md for the protein, the process > > stops withi

Re: [gmx-users] MPIRUN error while running position restrained MD

LINCS warning. > Besides, please be more specific in what you're > trying to simulate, > and what protocol you used. > > Cheers, > > Tsjerk > > On 1/19/07, Ragothaman Yennamalli > <[EMAIL PROTECTED]> wrote: > > Hi, > > This is the tail

Re: [gmx-users] MPIRUN error while running position restrained MD

contacts they would get resolved in minimization step, but looks like it hasn't. Please tell me how to solve this problem. Raghu --- Mark Abraham <[EMAIL PROTECTED]> wrote: > Ragothaman Yennamalli wrote: > > HI, > > Since the log files and crashed .pdb files had > filled &

Re: [gmx-users] MPIRUN error while running position restrained MD

Hi, I increased the tau_p to 2.0 and lincs-iter to 4. Now the system is running smoothly. Regards, Ragothaman --- Mark Abraham <[EMAIL PROTECTED]> wrote: > Ragothaman Yennamalli wrote: > > HI, > > Since the log files and crashed .pdb files had > filled > > the wh

Re: [gmx-users] MPIRUN error while running position restrained MD

Hi Tsjerk, I completely agree with you. I am treating symptoms rather than the problem. I read your previous comment on the LINCS warning to Shangwa Han. I dont have any unnatural amino acids in the protein and EM steps converged to machine precision. I am attaching the potential energy .xvg file a