RE: [gmx-users] Overflow problem with test-particle insertion

Hi, You should use the release-4-5-patches branch. After git clone do: git branch --track release-4-5-patches origin/release-4-5-patches git checkout release-4-5-patches Berk > Date: Thu, 9 Sep 2010 19:38:00 -0400 > From: kd...@princeton.edu > To: gmx-users@gromacs.org > Subject: [gmx-users] Ove

RE: [gmx-users] Overflow problem with test-particle insertion

Hi, I put in the negative energy check on purpose. There can be highly negative energies, which should not happen. So energies smaller than -50kT are ignored. But maybe such energies could only occur due to the SSE overflows and not during non-SSE computation. If that's the case this check could

[gmx-users] strange jumping in the frames

I am running Metadynamics with gromacs, I saw a jump in the frame after the simulation was running for a while, I copy here part of the log file: Step Time Lambda 2055750041115.00.0 Energies (kJ/mol) AngleProper Dih. L

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

Hi all, I just realized the the format of defining the atom-name in [atomtypes] section in ffnonbond.ipt in different forcefields are different. such as 1. oplsaa.ff/ [ atomtypes ] ; name  bond_type    mass    charge   ptype  sigma  epsilon  opls_001   C   6  12.01100 0.500

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

- Original Message - From: Baofu Qiao Date: Friday, September 10, 2010 18:38 Subject: [gmx-users] question about the format of [atomtypes] in ffnonbond.itp To: Discussion list for GROMACS users --- | > Hi all, > >

Re: [gmx-users] strange jumping in the frames

> as you can see the time jumped from > 41120.0 to 41125.00391 , > while it has to be 41125.0 and then it continue the rest of > simulation like this, > Do you what is the problem ?!! Probably no problem at all. Numbers that are readily represented in decimal notation, like a tim

[gmx-users] Protein out of the box (not PBC problem)

Hi everyone, please I can't figure out how to do this: I have a trajectory with water. If I concatenate it, since I have a FAT32 file system, it's a file too large! So I'm trying to avoid this. For that, I extracted my protein (it's a dimer) from each step of my simulation (when doing that, I di

Re: [gmx-users] Protein out of the box (not PBC problem)

- Original Message - From: Carla Jamous Date: Friday, September 10, 2010 19:15 Subject: [gmx-users] Protein out of the box (not PBC problem) To: Discussion list for GROMACS users > Hi everyone, > > please I can't figure out how to do this: > > I have a trajectory with water. If I con

[gmx-users] g_wham: "Pull geometry direction_periodic not supported"

Hi gmx-users I finished a series of pulling runs using the "periodic_direction" option and when I run the g_wham analysis I received the following message. --- Program g_wham, VERSION 4.5 Source code file: gmx_wham.c, line: 1369 Fatal error: Pul

Re: [gmx-users] g_wham: "Pull geometry direction_periodic not supported"

Eudes Fileti wrote: Hi gmx-users I finished a series of pulling runs using the "periodic_direction" option and when I run the g_wham analysis I received the following message. --- Program g_wham, VERSION 4.5 Source code file: gmx_wham.c, li

RE: [gmx-users] Overflow problem with test-particle insertion

Hi, I should read my own code comments better (usually Gromacs has too little comments, but I put one here). The lower bound check was because of issues with tabulated interactions. The problem was that the Gromacs generated tables (for e.g. LJ shift or PME) were zero for r<0.02 nm. Thus you co

[gmx-users] Checkpoint files not being written

Hi All, I don't know if this is a new (intended) feature or a bug, so I figured I'd ask :) I'm running version 4.5.1 to do some implicit solvent simulations. What I've noticed is that, no matter how long the simulation runs, I only ever get a checkpoint file at the end of the simulation, an

RE: [gmx-users] Checkpoint files not being written

Hi, Do you have no cut-off's and nstlist set to 0? That's the only case where I could see that checkpoints are missing. If that's the case, please file a bugzilla so we don't forget to fix this for 4.5.2. PS -cpnum has nothing to do with this. I guess it's the bCPT = assignment in md.c that onl

Re: [gmx-users] Checkpoint files not being written

With explicit solvent simulations I am still producing checkpoints as normal, maybe it has something to do with the implicit solvent settings? Cheers Tom On 10/09/10 16:08, Justin A. Lemkul wrote: Hi All, I don't know if this is a new (intended) feature or a bug, so I figured I'd ask :) I'm

RE: [gmx-users] Checkpoint files not being written

Hi, I guess you have nstlist=0. Try the fix below. Berk diff --git a/src/kernel/md.c b/src/kernel/md.c index dd92d51..225a4bb 100644 --- a/src/kernel/md.c +++ b/src/kernel/md.c @@ -1859,7 +1859,7 @@ double do_md(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[], * or at the l

Re: [gmx-users] Checkpoint files not being written

Berk Hess wrote: Hi, I guess you have nstlist=0. Try the fix below. Yes, that is the case. I was using settings to employ the accelerated all-vs-all kernel. The fix below works and I have produced a .cpt file at the appropriate time. Thanks for the quick fix. -Justin Berk diff --

[gmx-users] g_hbond solvent insertion problem

Hi all: I´m using gromacs version 4.0.2 and a box type truncated octahedron for the MD simulation. I need to analyze hydrogen bonds with solvent (water)insertion. I used the following command: g_hbond –f *.xtc –s *.tpr –n *.ndx –num num.xvg –dist *.xvg –ang *.xvg –a 45 –r 0.3 –ins. I selected accep

Re: [gmx-users] g_hbond solvent insertion problem

ceste...@unsl.edu.ar wrote: Hi all: I´m using gromacs version 4.0.2 and a box type truncated octahedron for the MD simulation. I need to analyze hydrogen bonds with solvent (water)insertion. I used the following command: g_hbond –f *.xtc –s *.tpr –n *.ndx –num num.xvg –dist *.xvg –ang *.xvg –a

[gmx-users] PDB will not minimize?

Downloaded a pdb from pdb.org (1HNX) and stripped the PCY ligand and plugged it into pdb2gmx using AMBER03 and TIP3P (GROMACS 4.5). Ran through the rest of my process and I am having some issues.   Here is my flow of commands:   pdb2gmx -f "$base".pdb -o "$base".gr

[gmx-users] please help, cannot compile gmx 4.5 openmm

I am doing, after compiling and installing the normal grmx 4.5: rm -fr CMakeCache.txt make clean export OPENMM_ROOT_DIR=/usr/local/openmm cmake -DGMX_OPENMM=ON .. make mdrun [ 1%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o [ 1%] Building

Re: [gmx-users] PDB will not minimize?

TJ Mustard wrote: Downloaded a pdb from pdb.org (1HNX) and stripped the PCY ligand and plugged it into pdb2gmx using AMBER03 and TIP3P (GROMACS 4.5). Ran through the rest of my process and I am having some issues. Here is my flow of commands: pdb2gmx -f "$base".pdb -o "$base".gro

[gmx-users] OWT5 not found in Charmmff

I am running tip5p in charmm force field in gmx. In energy minimization step, it gives an error msg as below. I just simply added it in atomtypes.atp in charmm27.ff, but still it doesn't work. Does anyone know how to solve it? Many thanks, Yao ---

Re: [gmx-users] PDB will not minimize?

  My appologies I have errors all over this. On September 11, 2010 at 12:44 AM "Justin A. Lemkul" wrote: > > > TJ Mustard wrote: > > > > > > Downloaded a pdb from pdb.org (1HNX) and stripped t

[gmx-users] Can gromacs developers write code to put an external force on atoms in a specified region in later versions?

Dear gromacs developers, As far as I know, in the latest gromacs version, one only can put an external force on a group of atoms, but can not put external force on atoms in a specific region, for instance, the region from z = 4 nm to z = 6 nm. Some other softwares like NAMD seem to have such fu