Re: [gmx-users] Re: ionic liquids

If you are sure about the force field (the one from Lopes et al.?) you are using, build a dilute system, and then run long enough simulations using NTP ensemble. possibly using simulation annealing. ? 2011-4-30 16:44, Vitaly Chaban ??: I am trying to create an ionic-liquid system

Re: [gmx-users] Important bugfix for g_hbond

bond2 -f T298 -s T298 -n -merge). Note that the value of 7217 is independent of -merge/-nomerge. I am using Gromacs 4.5.3 with your 'bugfix". Gromacs 4.0.7 give the similar value of about 7210 with -merge or -nomerge. ** Any suggestion is appreciat

[gmx-users] memory problem of g_hbond?

tion is some slab structure of thickness of about 3ns, where there is only ~3000 waters. Can someone give me some suggestions? Thanks a lot! best regards, Baofu Qiao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/

Re: [gmx-users] memory problem of g_hbond?

Thanks a lot, Erik! But could you specify how to build the index of water in certain region, say 0 On 05/23/2011 11:05 AM, Erik Marklund wrote: Baofu Qiao skrev 2011-05-23 10.47: Hi all, Very recently, I meet a problem when using g_hbond (gromacs 4.5.3 with the bugfixed

[gmx-users] residue number starting from not 1

99317Na Na 9299 12.146 5.676 14.924 -0.1802 -0.9861 0.2229 99318Na Na 9300 11.363 11.645 8.887 0.4524 -0.4644 -0.0401 ... .. ******** regards, Baofu Qiao -- gmx-users mailing listgmx-us

Re: [gmx-users] Residence time and trjorder

HI Carla, I wrote a similar code, see attached. But it is written for my condition. You should modify it accordingly. regards, Baofu Qiao On 07/12/2011 02:04 PM, Carla Jamous wrote: Dear gmx-users, I used trjorder in order to study the water molecules that are closer than 5 A from my

Re: [gmx-users] Connecting sidechains in gromacs file

are you sure that your topology file is correctly written? On 07/15/2011 11:34 AM, Zack Scholl wrote: Hi all - I'm running a simulation that has an implicit solvent. I ran my simulation and it seems that everything not connected to the backbone has floated off into space. Is there a way to de

[gmx-users] dihedral problem when converging Charmm FF into Gromacs format

the original Charmm FF, but not in Gromacs? Thanks a lot! BTW: the Phase terms are also not equal to each other! best wishes, Baofu Qiao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Sup

[gmx-users] question about positive potential

Hi all, After a 3ns MD run, I took a look at the  .log file, and found the potential is positive. How could it be?!  I wonder what is the problem.  The standard deviation of density is small, while the SD of potential is big. Is the system not equilibrated (if yes, why the sd of density is so

Re: [gmx-users] question about positive potential

this problem? and when the potential is positive, why doesn't the system becomes expanded (Does positive potential have some physics)? thanks in advance! best wishes, Baofu Qiao Mark Abraham wrote: > Baofu Qiao wrote: >> Hi all, >> >> After a 3ns MD run, I took

[gmx-users] question about continuation using tpbconv and mdrun -cpi

in the former section is identical to the reference) Then, how to reproduce exactly the potential? It is said that the continuation from "mdrun -cpi" is binary identical. However, it seems not in my tests. What's the problem of the very big RMSD of the potential from eneconv?

Re: [gmx-users] question about continuation using tpbconv and mdrun -cpi

ry for restarts without appending)." best wishes, Mark Abraham wrote: > Baofu Qiao wrote: >> Hi all, >> >> Recently I made some tests on the continuation of gmx 4.0.5. Firstly, I >> run a complete simulation as the reference. In the full.mdp file, >> gen_seed

Re: [gmx-users] question about continuation using tpbconv and mdrun -cpi

o full2 mpirun -np 32 mdrun -deffnm full2 -reprod yes -cpt 2 -maxh 0.2 mpirun -np 32 mdrun -deffnm full2 -reprod yes -cpi full2.cpt -append **** Do you have some further ideas? best wishes, Baofu Qiao Mark Abraham wrote: >

Re: [gmx-users] question about continuation using tpbconv and mdrun -cpi

Hi Berk, Thanks for pointing out my mistake! What I worry about is how big the deviation is after several continuations? If it is unpredictable, it is a sad news. regards, Baofu Qiao Berk Hess wrote: Hi, Your command line is incorrect. -reprod should be used without yes. -reprod is yes

[gmx-users] question about mdrun -append

Hi all, I meet one problem when I am using mdrun -append. In some cases, the following error information happens, and mdrun is halted * Program mdrun, VERSION 4.0.5 Source code file: checkpoint.c, line: 1248 Fatal error: Truncation of file T298.xtc f

Re: [gmx-users] question about mdrun -append

Hi Berk, Thanks for your reply!  The result of  "gmxdump -cp T298.cpt" is given as follows (the long list of x, v, E is not shown) ** number of output files = 4 output filename = T298.log file_offset_high = 0 file_offset_low = 7228659 output filename = T298.

Re: [gmx-users] question about mdrun -append

put lines " /usr/bin/install -c -m 644 './ngmx.1' '/data1/HLRS/dgrid/stbw0172/programes/gromacs-4.0.5/bin//share/man/man1/ngmx.1'" says that the latest mdrun is installed in the right folder. Is there something wrong in the above process? or some further suggestions? t

Re: [gmx-users] question about mdrun -append

Hi Berk, Now it works. I copy the mdrun manually to the $GMX/bin folder.  I checked the date of mdrun, and find that "mdrun -install mdrun" doesn't copy the latest mdrun file to $GMX/bin folder. Thank a lot for you help! regards, Baofu Qiao Berk Hess wrote: Strange...

[gmx-users] question about the implicit walls

for?  I guess it is based on a lattice model. If I want to build silicon or graphene walls, what kind of values is suitable for them? Any reference? regards, Baofu Qiao [gmx-users] Implicit walls. Yves Dubief Thu, 11 Jun 2009 03:32:11 -0700 Hi, I am using the implicit wall method available in 4.0

Re: [gmx-users] question about the implicit walls

uot; for? I guess it is based on a lattice model. If I want to build silicon or graphene walls, what kind of values is suitable for them? Any reference? regards, Baofu Qiao [gmx-users] Implicit walls. Yves Dubief Thu, 11 Jun 2009 03:32:11 -0700 Hi, I am using the implicit wall m

Re: [gmx-users] g_density options

For a homogenious system, you can also use g_density: g_density -sl 1 -dens mass -f -s -o Mark Abraham wrote: You get the density by running g_energy. If you've tried that and seen that the density wasn't there, that would be because your volume is constant in an NVT simulation. grompp pro

[gmx-users] Failed to lock: pre.log (Gromacs 4.5.3)

Hi all, I got the error message when I am extending the simulation using the following command: mpiexec -np 64 mdrun -deffnm pre -npme 32 -maxh 2 -table table -cpi pre.cpt -append The previous simuluation is succeeded. I wonder why pre.log is locked, and the strange warning of "*Function not impl

[gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)

Hi all, I just recompiled GMX4.0.7. Such error doesn't occur. But 4.0.7 is about 30% slower than 4.5.3. So I really appreciate if anyone can help me with it! best regards, Baofu Qiao 于 2010-11-25 20:17, Baofu Qiao 写道: > Hi all, > > I got the error message when I am extending

Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)

Qiao On 11/26/2010 09:07 AM, Carsten Kutzner wrote: > Hi, > > as a workaround you could run with -noappend and later > concatenate the output files. Then you should have no > problems with locking. > > Carsten > > > On Nov 25, 2010, at 9:43 PM, Baofu Qiao wrote:

Re: [gmx-users] system is exploding

can you advice me on this, what > I need to check. > > best, > > Olga > > -- Dr. Baofu Qiao Institute for Computational Physics Universität Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49(0)711 68563607 Fax: +49(0

Re: [gmx-users] system is exploding

If you are really sure about the topology, the problem is the initial structure. Try to use PackMol to build it. On 11/26/2010 11:42 AM, Olga Ivchenko wrote: > I tried today to run minimization in vacuum for my small molecules. This has > the same error. > > 2010/11/26 Baofu Qiao &g

Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3) Neither of 4.5.1, 4.5.2 and 4.5.3 works

help? Thanks a lot! best regards, On 11/26/2010 09:07 AM, Carsten Kutzner wrote: > Hi, > > as a workaround you could run with -noappend and later > concatenate the output files. Then you should have no > problems with locking. > > Carsten > > > On Nov 25, 2010

Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)

Hi Roland, Thanks a lot! OS: Scientific Linux 5.5. But the system to store data is called as WORKSPACE, different from the regular hardware system. Maybe this is the reason. I'll try what you suggest! regards, Baofu Qiao On 11/26/2010 04:07 PM, Roland Schulz wrote: > Baofu,

Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3)

de more information about the file system? > The command "mount" provides the file system used. If it is a > network-file-system than the operating system and file system used on the > file server is also of interest. > > Roland > > On Fri, Nov 26, 2010 at 11:00 AM, Baof

Re: [gmx-users] Re: Failed to lock: pre.log (Gromacs 4.5.3): SOLVED

ake things short. The used file system is lustre. /Flo On 11/26/2010 05:49 PM, Baofu Qiao wrote: Hi Roland, The output of "mount" is : /dev/mapper/grid01-root on / type ext3 (rw) proc on /proc type proc (rw) sysfs on /sys type sysfs (rw) devpts on /dev/pts type devpts (rw,gid=5,mode=62

Re: [gmx-users] changing the velocity in trajectory file

Why don't use different random (gen_vel =yes; gen_seed =-1 in .mdp file) seed to generate the velocity? On 11/29/2010 02:55 PM, sreelakshmi ramesh wrote: > Dear all, > could anybody help me out with the following issue. I have a > trajectory file.i have to used that file at a par

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

not found line 45: ./coarse_grain.tcl: line 120: syntax error near unexpected token `}' '/coarse_grain.tcl: line 120: ` } else { best wishes, Baofu Qiao Nicolas SAPAY wrote: Justin A. Lemkul wrote: I have also added a Perl script to the GROMACS site (the VMD page): http://www

[gmx-users] 10-4-3 implicit wall potential

HI all, Does anyone have experience to implement the 10-4-3 implicit wall potential? If I want to use it, which files do I need to change, except wall.c? Can anyone give some suggestions? Thanks a lot! best wishes, Baofu Qiao -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] SiO2 simulation

. regards, Baofu Qiao Justin A. Lemkul wrote: Arden Perkins wrote: I believe pdb files (protein data bank) are only for peptides, so unless you are simulating a peptide you will not need any pdb files for your There are numerous utilities that generate .pdb files; it is not true to say that

[gmx-users] question about the Silicon force field in gromacs

, Langmuir, 2006, 22, 5666.), I think you might be able to give me some help. Thanks a lot! best wishes, Baofu Qiao -- 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

Re: [gmx-users] 10-4-3 implicit wall potential

table_SOL_wall0/wall1, the answer of the 3rd question (cutoff value for the tabulated potential calculation) should be 3nm, right? Sorry for the lots of questions! best wishes, Baofu Qiao Berk Hess wrote: Hi, Why not use the tabulated wall potential? That does not require are changes to

Re: [gmx-users] 10-4-3 implicit wall potential

Hi, Thanks a lot! I just tried again. "mdrun -table table" works. best regards, Baofu Qiao Berk Hess wrote: > Hi, > > Do you really need all those tables? > I would think you onkly need to specify your wall table and no other tables. > > As the documentation says (I

[gmx-users] implicit wall doesn't recognize the wall_atomtype correctly?

  = 2 wall_type    = 9-3   wall_r_linpot   = 0.1 wall_atomtype    = abc   123    ;opls_abc  opls_abc wall_density   = 144 144 wall_ewald_zfac    = 3 best wishes, Baofu Qiao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

[gmx-users] strange empty space inside the system box

Hi all, Is there anyone who can give me some suggestions? My system is composed of some polymer chains and waters. The density of the solution is about 1g/cm^3. Then I added two explicit grahpite layers (resname=WAL) at the bottom and top of the solution, which are both freezed in three dimen

Re: [gmx-users] strange empty space inside the system box

the empty space is not there. Any other idea about it? best regards, Baofu Qiao chris.ne...@utoronto.ca wrote: Sounds like a bubble. Do some NpT equilibration by adding pressure coupling. That's going to be difficult with your freeze groups though. Basically, you need to find a way to ge

Re: [gmx-users] RE: xmgrace

mdrun -s topol.tpr BTW: take a look at "mdrun -h " bharat gupta wrote: > Thanks sir > > But there is one problem that when I am running the mdrun step of 5th > step of lysozyme tutorial, I am getting an error :- > > Can not open file: > topol.tpr > > Can u tell me how to rectify it .. > --

[gmx-users] how to extract the LJ interaction parameters from the tpr file

"top.atoms.atom[index[i]].q", I have no idea how to get the LJ parameters of the atoms? Does anyone know how to get them from the top.atoms.atomXXX? Or is there some similar code to calculate such energies? Thanks in advances! Best wishes, Baofu Qiao -- gmx-users mailing listgmx-users@g

Re: [gmx-users] best interval for saving configurations ?

Hi, it depends. Firstly how strong are the configurations related over time. Then the maximum of your harddisk. Generally it is in the order of magnitude of ps. shahab shariati wrote: > Hi all > > > > What is the best interval for saving configurations in full md step? (every > what ps?) > >

Re: [gmx-users] how to extract the LJ interaction parameters from the tpr file

or me, because I want to calculate the energy terms based on the distance, which is not the cutoff distance in the simulations, but one from RDF calculation. regards, Baofu Qiao Mark Abraham wrote: > On 08/02/10 21:03, Baofu Qiao wrote: >> Hi all, >> >> I want to calculate t

[gmx-users] question about Gromacs and Spectroscopy

Hi all, I want to reproduce some experimental data on Spectroscopy using Gromacs. I want to know is it possible? If yes, how to do that? Is there any tutorial related to that? Any help is appreciate! regards, Baofu Qiao -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] question about Gromacs and Spectroscopy

red. I wonder whether I can reproduce it or not? I hope this is bit of clearer! Thanks a lot! regards, Baofu Qiao Justin A. Lemkul wrote: > > Baofu Qiao wrote: >> Hi all, >> >> I want to reproduce some experimental data on Spectroscopy using >> Gromacs. I want to kn

Re: [gmx-users] the job is not being distributed

I think this is not a problem of Gromacs, but the cluster you are using. Try to contact with your cluster administrator, and check the administration software. Syed Tarique Moin wrote: > Hi, > > I am using MPICH2 library for gromacs. > > Thanks and Regards > > Syed Tarique Moin > > > > >

Re: [gmx-users] Precision in trajectory file

The number of digits in .gro( or .pdb) is crudely fixed because of the format. Otherwise, it cannot be recognized by other softwares, like VMD. For the .trr files, I guess, if you are indeed running double-precision GMX, the leap-frog integrator is using double-precision coordinates, but the prin

[gmx-users] question about the format of [atomtypes] in ffnonbond.itp

c12 P5 72.0 0.000 A 0.0 0.0 I wonder how gromacs deals with these difference smartly? And if I want to write my force field files,  what should I pay attention to this difference? best wishes, Baofu Qiao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] ARG Charmm gmx 4.5.1

You should change the charge group number. Every charge group include several, like 3-4, atoms. Actually, the definition of charge group is not significant if you use PME for the coulomb interaction. nahren manuel wrote: > Dear Gromacs Users, > > I am using plain cutoff for my 12-mer protein. >