[gmx-users] nstlist with vdw only

Would't this mean, that molecules could suddenly appear and lead to a discontinuity in the LJ-potential? Or in what way should I modify the r_vdw according to what rlist? I wanna end with a cut-off of the LJ-potentail around 1.75nm. Thanks in advance Nicolas Erik Lindahl wrote: Hi Nicholas,

RE: [gmx-users] Residue abbreviation list with explanations

> > Could you please help me to find a Residue abbreviation list web site. If you want to find out what people are calling a particular molecule or residue, best place to look is the PDB Database. If it is a small molecule, then http://alpha2.bmc.uu.se/hicup/ is a good place to look. However, a

Re: [gmx-users] Residue abbreviation list with explanations

Sagittarius wrote: Dear Gromacs users, Could you please help me to find a Residue abbreviation list web site. I need to replace UNK below with something meaningful. formaldehyde.pdb looks like this: COMPNDUNNAMED REMARK 1 PDB to MMOD

Re: [gmx-users] PME or SPME?

Jones de Andrade wrote: Hi all. Well, I have some kind of a "didatic" doubt: Ok, from what I can understand up to now, PME uses lagrande interpolation for the genaration of the grid, while SPME uses cardinal B-splines to do so. Is it correct? And if, so, gromacs implements PME or SPME (the m

[gmx-users] Residue abbreviation list with explanations

Dear Gromacs users, Could you please help me to find a Residue abbreviation list web site. I need to replace UNK below with something meaningful. formaldehyde.pdb looks like this: COMPNDUNNAMED REMARK 1 PDB to MMOD atom-numbe

RE: [gmx-users] how to get CVS version gmx?

http://wiki.gromacs.org/index.php/CVS_HowTo Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the

[gmx-users] PME or SPME?

Hi all. Well, I have some kind of a "didatic" doubt: Ok, from what I can understand up to now, PME uses lagrande interpolation for the genaration of the grid, while SPME uses cardinal B-splines to do so. Is it correct? And if, so, gromacs implements PME or SPME (the manual states PME, but also st

Re: [gmx-users] nstlist with vdw only

Hi Nicholas, nstlist=1 means you recalculate the neighborlist every single step, which will be quite expensive. Depending on the type of system and temperature you are simulation you probably want to start somewhere around nstlist=10. Cheers, Erik On Aug 20, 2007, at 10:26 PM, Nicolas

[gmx-users] nstlist with vdw only

Hello again, just a quick question: my simulation runs with vdwtype = cut-off and no charges, so in my understanding I can set rcoulomb to whatever I want, since there is nothing that's got to be calculated. Within this configuration (rlilst = r_vdw, nstlist = 1) up to 50% of the computation

[gmx-users] Re: gromacs-gaussian interface compilation - HOW-TO?

Hi, Please post questions like this to the mailing list, so the answers make it to the archive. For QM/MM, have a look at http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ggroenh/ qmmm.html Unfortunately we are not even allowed to distribute a "diff" file with modifications to G

[gmx-users] [Fwd: gromacs-gaussian interface compilation - HOW-TO?]

>Hi, i want to know the procedure to compile the gromacs-gaussian 03 >interface. Can u please give me a link to the installation instructions >of gromacs-gaussian 03 interface. I sifted through the gromacs mailing >list and google before sending you this question. I am trying to >compile >on li

Re: [gmx-users] Error using double precision

[EMAIL PROTECTED] wrote: Ok (you didn't say that in the first mail...). Does it also happen on one processor? I Haven't tested in d.p. After how many steps does it happen? (see Marks mail). after 30 steps, that is 600 ps. I energy minimized the system in d.p. and it is still running aft

[gmx-users] topolbuild: attempt at a Gromacs topology builder added to Gromacs user contributed software

I got frustrated with the options for building topologies for ligands and wrote this to allow me to use bond length and angle values derived from prior modeling and NMR data. There probably will be something better than this from the developers at some point, but I decided to upload what I have t

Re: [gmx-users] Error using double precision

[EMAIL PROTECTED] wrote: Ok (you didn't say that in the first mail...). Does it also happen on one processor? I Haven't tested in d.p. After how many steps does it happen? (see Marks mail). after 30 steps, that is 600 ps. I energy minimized the system in d.p. and it is still running aft

Re: [gmx-users] Error using double precision

> >Ok (you didn't say that in the first mail...). > >Does it also happen on one processor? > > I Haven't tested in d.p. > > >After how many steps does it happen? (see Marks mail). > > after 30 steps, that is 600 ps. > > > I energy minimized the system in d.p. and it is still running after

Re: [gmx-users] Error using double precision

[EMAIL PROTECTED] wrote: Ok (you didn't say that in the first mail...). Does it also happen on one processor? I Haven't tested in d.p. After how many steps does it happen? (see Marks mail). after 30 steps, that is 600 ps. that means the trajectory is quite different from SP. I energ

[gmx-users] Error using double precision

>Ok (you didn't say that in the first mail...). >Does it also happen on one processor? I Haven't tested in d.p. >After how many steps does it happen? (see Marks mail). after 30 steps, that is 600 ps. I energy minimized the system in d.p. and it is still running after 710 ps. _

Re: [gmx-users] Error using double precision

[EMAIL PROTECTED] wrote: edvin.erdtman at nat.oru.se wrote: I installed both double and single precision gromacs on a new system. When running a membrane MD with double precision 8 processor mpi calc, this error appars in the error output file: this usually means you have an unequilibrated s

Re: [gmx-users] Error using double precision

[EMAIL PROTECTED] wrote: edvin.erdtman at nat.oru.se wrote: I installed both double and single precision gromacs on a new system. When running a membrane MD with double precision 8 processor mpi calc, this error appars in the error output file: this usually means you have an unequilibrated s

[gmx-users] Error using double precision

>edvin.erdtman at nat.oru.se wrote: >> I installed both double and single precision gromacs on a new system. When >> running a membrane MD with double precision 8 processor mpi calc, this error >> appars in the error output file: > > >this usually means you have an unequilibrated system. But it

Re: [gmx-users] Error using double precision

[EMAIL PROTECTED] wrote: I installed both double and single precision gromacs on a new system. When running a membrane MD with double precision 8 processor mpi calc, this error appars in the error output file: this usually means you have an unequilibrated system. Error on node 4, will try

Re: [gmx-users] Step size too small

17 aug 2007 kl. 21.46 skrev TJ Piggot: Hi, I do not think that what Per suggests is the problem, if you look at the potential energy after the minimisation this value is huge (and the other two values are inf!). The problem is most likely with your topology. As you say the two molecules

Re: [gmx-users] Pull code methods?

I'm no umbrella user, but as far as I know, you have to set different parameters, according to the manual. These may be similar to the AFM parameters, but still, in the config file, they are separated. Sure, you don't define a pull rate for Umbrella, because you build, as you said, discrete syst

[gmx-users] Error using double precision

I installed both double and single precision gromacs on a new system. When running a membrane MD with double precision 8 processor mpi calc, this error appars in the error output file: Error on node 4, will try to stop all the nodes Halting parallel program mdrun_mpi_d-0(mpi:[EMAIL PROTECTED]) o