Re: [gmx-users] Minimum distance between periodic images

Thank you sir. On Tue, Oct 22, 2013 at 2:48 PM, Tsjerk Wassenaar wrote: > Hi Nidhi, > > These are periodicity artifacts. Make sure that you remove jumps over PBC > from your trajectory by using trjconv -pbc nojump. > > Cheers, > > Tsjerk > > > On Tue, Oct 2

[gmx-users] Minimum distance between periodic images

Dear all users I have simulated a protein with two chains (153 residues each) for 50ns(restarting crashed run 3 times) using a cubic box with each side as 11nm. After finding the closest distance between the periodic images, I found that the closest distance becomes lesser than 1 after 23ns for f

Re: [gmx-users] Re: g_hydorder

read following link: http://www.gromacs.org/Developer_Zone/Redmine But could not locate link to file redine issue. On Wed, Oct 2, 2013 at 12:41 AM, David van der Spoel wrote: > On 2013-10-01 19:51, Nidhi Katyal wrote: > >> Please provide me with necessary guidance. I have already

[gmx-users] Re: g_hydorder

Please provide me with necessary guidance. I have already posted this thrice but have not got a single reply Thanks in advance. On Tue, Oct 1, 2013 at 3:40 PM, Nidhi Katyal wrote: > Hello everyone, > > I would like to calculate angle tetrahedral order parameter of water > molecule

[gmx-users] g_hydorder

Hello everyone, I would like to calculate angle tetrahedral order parameter of water molecules as defined by Chau et al (eq 3). I am using g_hydorder of gromacs 4.6.3 with my index group containing all oxygen atoms of water: g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out file_

Re: [gmx-users] restarting the crashed run

-noappend trjcat -f previous.trr next.trr -o combine.trr On Sun, Sep 22, 2013 at 1:43 AM, Justin Lemkul wrote: > > > On 9/21/13 3:46 PM, Nidhi Katyal wrote: > >> Dear all >> I would like to know the difference between restarting our crashed runs by >> 1) f

[gmx-users] restarting the crashed run

Dear all I would like to know the difference between restarting our crashed runs by 1) first generating next.tpr using tpbconv -extend option then running grompp with this *.tpr file and finally running mdrun but with no cpi option 2) same as 1 but with -cpi option 3) using only mdrun comma

[gmx-users] question about g_hydorder

Hello, I would like to calculate angle tetrahedral order parameter of water molecules as defined by Chau et al (eq 3). I am using g_hydorder of gromacs 4.6.3 with my index group containing all oxygen atoms of water: g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out file_2.out -n i

Re: [gmx-users] question about g_hbond

I have created my files long time ago using version 4.0.7. But now analyzing the same files using g_hbond/g_mindist using version 4.5.5 On Sun, Sep 1, 2013 at 10:48 PM, Justin Lemkul wrote: > > > On 9/1/13 1:17 PM, Nidhi Katyal wrote: > >> Even after giving same cutoff radius

Re: [gmx-users] question about g_hbond

Even after giving same cutoff radius of 0.35nm in both, I am getting around 400 contacts per timeframe with mindist but 0 contacts with g_hbond. On Sun, Sep 1, 2013 at 10:40 PM, Justin Lemkul wrote: > > > On 9/1/13 1:08 PM, Nidhi Katyal wrote: > >> The two groups are: pro

Re: [gmx-users] question about g_hbond

The two groups are: protein and cosolvent molecules. With g_mindist -on , I am getting values of around 6500 per timeframe. But then why g_hbond giving different results. On Sun, Sep 1, 2013 at 10:23 PM, Justin Lemkul wrote: > > > On 9/1/13 12:50 PM, Nidhi Katyal wrote: > >>

[gmx-users] question about g_hbond

Hello, I would like to calculate number of contacts between two groups, for which I am using following command: g_hbond -f *.xtc -s *.tpr -num *.xvg -contact -b 49000 -e 5 I am getting 0 as the output. But when I am calculating number of hydrogen bonds between the same two groups by using the a

[gmx-users] question about g_hydorder

Dear all I would like to calculate angle tetrahedral order parameter of water molecules as defined by Chau et al (eq 3). I am using g_hydorder of gromacs 4.6.3 with my index group containing all oxygen atoms of water: g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out file_2.out -n

[gmx-users] g_hydorder error

Dear all, I am using following command in gromacs version 4.5.5: g_hydorder -f *.xtc -s *.tpr -n *.ndx -o file1.xpm file2.xpm But getting following error: Internal error in pbc_dx, set_pbc has not been called In my mdp file, I have set pbc to xyz I have searched the archive and found that simila

[gmx-users] trjorder

Dear all I would like to know the number of oxygen atoms of my co-solvent molecules which are around 0.3nm of the protein in the last few ns. I have read the manual and found that trjorder could serve the purpose. So i have first created index file containing all the oxygen atoms of my co-solvent m

Re: [gmx-users] HB lifetime

g went wrong that > should be changed. Again, did you *look* at the acf? > > Erik > > 30 mar 2012 kl. 11.53 skrev Nidhi Katyal: > > for another system (at 250K) also i have calculated hydrogen bond lifetime > using: > hbond -f *.xtc -s *.tpr -ac *.xvg -num *.xvg -life *

Re: [gmx-users] HB lifetime

lifetime mean? Thank you in advance. On Thu, Mar 29, 2012 at 12:56 PM, Erik Marklund wrote: > > 29 mar 2012 kl. 18.47 skrev Nidhi Katyal: > > Dear All > I would like to know the strength of the given bond by calculating the > lifetime of that bond.For the same reason i used: >

[gmx-users] HB lifetime

Dear All I would like to know the strength of the given bond by calculating the lifetime of that bond.For the same reason i used: g_hbond -f *.xtc -s *.tpr -ac *.xvg -temp 300 -num *.xvg -life *.xvg and i got: TypeRate(1/ps) Time(ps) ... Forward-0.182-5.495 ... HB lifetime

[gmx-users] addition of two solvents

Dear all I would like to insert two co-solvents in box along with the protein.Please suggest me the command to do so. In genbox there is only one flag -ci to insert extra molecule.How to insert one more type of molecule? Thank you in advance. -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] cannot determine precision of trn file

I think my restart was achieved successfully as my err file contained following lines: "reading checkpoint file state.cpt generated: Loaded with memory making 2D domain decomposition 4*2*1 starting mdrun 'protein in water' 1500 steps, 3.0ps(continuing from step 1500, 3.0ps)." Also

[gmx-users] cannot determine precision of trn file

Dear All, I was running my simulation for 30ns but at the last step i got following error: "Cannot close energy file;it might be corrupt, or maybe you are out of quota." It was found that there was some disk space problem but when the issue was resolved i restarted my run from the last step using

[gmx-users] water radial distribution function

Dear all, I would like to plot g(OO) water radial distribution function.How should i use g_rdf or any other command to do this?Please help. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Su

[gmx-users] isodensity surface

Thank you for your reply.I was able to create isodensity surface but can i color my protein surface according to the difference in flexibility of the backbone caused by addition of some molecule and also know addition of which molecules.Please help. -- gmx-users mailing listgmx-users@gromacs.

[gmx-users] isodensity surface

Dear all, Is there a way to create and visualize isodensity surfaces in Gromacs or any tool which can work on gromacs compatible file? Any suggestion would be highly welcomed. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the a

[gmx-users] isodensity surface

Dear all, Is there a way to create and visualize isodensity surfaces in Gromacs or any tool which can work on gromacs compatible file? Any suggestion would be highly welcomed. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the a

[gmx-users] (no subject)

Dear all, I am trying to create tmao box.Energy minimization, simulated annealing (Cooling under high pressure and again heating at normal pressure) as well as final equilibration ran smoothly. But finally I got a box where all water molecules got accumulated in two three small region within the bo