[gmx-users] Alternating electric fields in GROMACS

manual says "not implemented yet". Best regards, Bert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscr

[gmx-users] How to compile the template.c when GMX is builded with cmake

Dear all, When GMX is builded with cmake, how to compile the template.c? I used to make the template.c by the command "make -f MakefileXXX", but it can not work in version 4.5. Thanks for your suggestions. Best regards, Bert -- gmx-users mailing listgmx-users@gromac

[gmx-users] g_hbond in 4.5.4 gives wrong output

Dear all, g_hbond of gromacs4.0.7 and 4.5.4 gives different outputs in average hbond number. Is there any fix to g_hbond of 4.5.4? Any suggestions are appreciated. Bests, Bert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] How to compile/run Gromacs on native Infiniband?

one gets much higher throughput and lower latency, while spending less CPU on networking. Therefore, I wonder if Gromacs has the native IB verbs interface. If so, how to compile and run Gromacs on native Infiniband? Any suggestions will be appreciated. Best Regards, Bert -- gmx-users mailing

[gmx-users] mdrun did not support large file offsets

Dear gmx-users, When I continued a run on my x86_64 linux clusters using the command "mdrun -deffnm prod -cpi prod.cpt -append", I got the errors as below: Program mdrun, VERSION 4.5.4 Source code file: checkpoint.c, line: 1734 Fatal error: The original run wrote a file called 'prod.xtc' which

[gmx-users] RE: mdrun did not support large file offsets

Dear all, When I compile gromacs using cmake, no large file related option was found in the cmake interface, however, I found the option for large file support in the CMakeCache.txt listed as bellow. . //Result of TEST_BIG_ENDIAN GMX_INTEGER_BIG_ENDIAN:INTERNAL=0 //Result of test for large fil

[gmx-users] Test suit failures

are obvious. Any suggestion would be appreciate. Thank you. Best Regards, Bert ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting

[gmx-users] Center of Mass removal in a specified direction

during long time simulations. I wanna know if there is a solution for this case. Any suggestions will be appreciated. Best regards, Bert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support

[gmx-users] absolute reference for pulling and center of mass removal

tem. The polymer and the water flowed in the negative direction. 2) Set comm-grps = polymer SOL. The polymer still moved in x, and no COM motion observed for SOL. Which one could be appropriate, and if both are not ok, is there a way to solve the problems? Thanks for your suggestions in advance!

[gmx-users] Question about Wall Potential

Dear gmx-users, I want to know the the specified form for the 10-4 wall potential in GROMACS. I assume it is: VLJ = C12*density*/z^10 - c6*density*/r^4 Am I right? If not, please correct me. Thanks for your suggestions in advance. Bests, Bert -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Crashes caused by particles communicated to PME node

Hi gmx-users, My system has a 7*7*22 box and 3dc geometry for PME is applid (large vacuum space is in the z direction. I found a crash caused by particles communicated to PME node. Note that this problem had a fix already ( http://www.gromacs.org/component/option,com_wrapper/Itemid,90/), I was afr

[gmx-users] Force constant defined in flexible TIP3P water model

equivalent to 443153 kJ/mol/nm^2 and 285 kJ/mol/rad^2, respectively. These two values are inconsistent with the corresponding values in tip3p.itp, which gives 502416.0 kJ/mol/nm^2 for bond and 628.02 kJ/mol/rad^2 for angle. I wanna know which one will be ok to use. Thanks for your attention. Bert

[gmx-users] Re: GMX 4.0 RC2: mdrun writes broken molecules?

I have encountered the same problem too. For water molecules not being broken in the mdrun, I think atoms in same charge group will not be divided into separate processors. It will be ok to use trjconv -pbc nojump/mol to get a clear visualization. > > Hi Justin, > > It's indeed the case that mdru

[gmx-users] How to make a soft repulsive potential wall

Hi gmx-users, I was simulating a water-surface system recently. The water molecules will escape from the solid surface, evaporate into the vacuum space above the surface, probably never come back and be trapped into the underpart of the surface for periodicity. I want to prevent the evaporating wa

[gmx-users] Walls & user defined potential

Hi gmx-users and developers, I met a strange error when using wall function combined with user defined potential. Following is a part of the mdp: vdw-type = user energygrps = Surf SOL ; WALLS

[gmx-users] inconsistent shifts

Hi all, I use pbc=full in my system, and all runs are ok except for the "inconsistent shifts" warnings when I use some analysis tools, such as g_density, g_densmap, etc. I have searched the whole list related to this problem, and I doubt several analysis tools are not coded with consideration of f

[gmx-users] Re: gmx-users Digest, Vol 48, Issue 24

Thanks David. There still "inconsitent shifts" warnings with a tpr made by pbc=xyz. By the way, my itp file is not changed, that is, the bonded terms between periodic images are still in the topology. Should I make a topology with pbc=xyz too? > > Bert wrote: > > Hi all,

[gmx-users] query about .xpm file

file, but I can not set the coordinates of the ticks with regular integers. Thanks very much for suggestions. Bert ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] force field parameters for hydronium

Hi gmx-users, I wonder if I can add H3O+ (Eigen) and OH- combined with SPC/E water model into my system. I have not found any available force field parameters for them in gmx yet, does anyone has itps and gros file for modeling them? BTW, I do not care about the PH value, and I only treat them as

[gmx-users] PME 3dc geometry and the optimal PME mesh load

Hi all, I use 3dc geometry for a system with large box size in z direction, and when I try the new CVS version, I find a note saying "The optimal PME mesh load is usually between 025 and 0.33, you should probably increase the cut-off and the PME grid spacing". A quite large estimation 0.86 was rep

[gmx-users] Error when compiled with fortran compiler in double precision

ot; The naming of these header files are not consistent with the file name in dir nb_kernel_f77_double. Obviously an underline is lost here. I hope this issue will be fixed soon. Version: Gromacs-4.5b3 and the latest git vesion Command: configure --disable-float --enable-fortran ... B

Re: [gmx-users] analysizing the sam.edo script?

e! > > I don't seem to have a local copy of parse_edo, but .edo files are ascii text files that can be readily parsed with standard tools like awk. Bert ______ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomol

[gmx-users] Re: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue

seems a perfectly valid suggestion to me. What's your doubt? Bert __ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goettingen, Germany tel: +49-551-2012308, fax: +4

Re: [gmx-users] how to fix a position in the single eigenvector in essential dynamics sampling?

xi zhao wrote: > Dear users: > I want to know: in EDS (essential dynamics sampling), how to fix the > eigenvector ,while the other degrees of freedom wiil be equilibrated. > how to set up? using the :linfix" in make_edi ? yes, "linfix" with stepsize zero for the

Re: [gmx-users] rotational fit in XY plane only

ual? (you may get a problem with mirror images, but the handedness is anyway not anymore uniquely defined once you project on 2D). Bert __ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics gro

Re: [gmx-users] NMA for a group

licit solvent. right. one way to include water and still have a manageable system size is to work with a small droplet of explicit water. Bert __ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg

Re: [gmx-users] NMA for a group

Mark Abraham wrote: > Christian Seifert wrote: >> On Friday 22 June 2007 10:59, Bert de Groot wrote: > >> The hessian is the second (numerical) derivative of the atoms in the >> three dimensions. In the future, I want to calculate the hessian of >> molecules n

Re: [gmx-users] essential dynamics

gromacs as well: again make_edi -h or http://www3.interscience.wiley.com/cgi-bin/abstract/112750179/ABSTRACT cheers, Bert __ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goet

Re: [gmx-users] Doubt about -linfix, -linacc, -radfix, -radacc, -radcon

the string options for > these algorithms see example above > and which one should I use? that we cannot answer for you. It all depends on the question you're trying to address with these simulations. Bert __ Bert de Groot, PhD Max Planck In

Re: [gmx-users] Reading XTC files from fortran90

don't know what happens if you read&write from the same file. Bert On Sat, 29 Sep 2007, Jones de Andrade wrote: > Hi all. > > I'm writing this beucase I'm having terrible problems in trying to deal with > gromacs trajectory files with my own programs, origina

Re: [gmx-users] Reading XTC files from fortran90

On Sat, 29 Sep 2007, Jones de Andrade wrote: > Hi Bert. > > Thank you for the prompt answer. > > Just did as instructed, but got the following: > > CruNumMac src/own/B/9/xtc 286% ifort xtciof.f90 test_xtc.f90 > -L/home/johannes/src/own/B/9/xtc/xtc/ -lxrdf -lg2c > IP

Re: [gmx-users] normal mode analysis

two protein-only trajectories, on which you then can run a PCA with g_covar (either separately and calculate eigenvector overlaps, or concatenate both trajectories and look at projection differences). best, Bert __ Bert de Groot, PhD Max Planck Institute for B

Re: [gmx-users] Essential Dynamics Sampling (EDS) MD

;t post? Read http://www.gromacs.org/mailing_lists/users.php . -- Bert __ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goettingen, Germany tel: +49-551-2012308, f

Re: [gmx-users] Essential Dynamics Sampling (EDS) MD

Ran Friedman wrote: Dear Bert, The Jacobi error hints at a fitting problem. If not the starting position, could it be the target that's causing the problems? Please check the head of the .edo and log files, to see if the reported RMSD's are what you would expect and especially i

Re: [gmx-users] loss of information trr xtc

Joern Lenz wrote: > hi guys. > can anyone tell me if there is a loss of information when i convert a trr > file > into a less-storage-consuming xtc file ? > can i reconevrt the xtc file into trr again and then have no loss of > information ? > thanks for a very short an