[gmx-users] error : One of the box lengths is smaller than twice the cut-off length

Dear All , I am getting following error while trying the energy minimization by using following command gromacs-4.5.5/proj1% grompp -v -f minim.mdp -c protein-solvated.pdb -p protein.top -o protein-EM-solvated.tpr *ERROR 1 [file protein.top, line 6486]:* ERROR: One of the box lengths is

[gmx-users] calculating lennard-jones interaction

hi dear users  wanna know if the distance between two species is more than the cut off radius of vdw interaction (in a SMD simulation), can we trust the simulation results? I mean what is the difference between this case and the situation that the cut off radius is lower than the distance

Re: [gmx-users] calculating lennard-jones interaction

Hi, Could you rephrase the question? Distance larger than cut-off and cut-off is less than distance seem equal by definition to me. Best, Erik 13 nov 2012 kl. 10.50 skrev Zahra M: hi dear users wanna know if the distance between two species is more than the cut off radius of vdw

[gmx-users] Re: Question about scaling

Am 13.11.2012 06:16, schrieb gmx-users-requ...@gromacs.org: Dear all, i did some scaling tests for a cluster and i'm a little bit clueless about the results. So first the setup: Cluster: Saxonid 6100, Opteron 6272 16C 2.100GHz, Infiniband QDR GROMACS version: 4.0.7 and 4.5.5 Compiler: GCC

[gmx-users] Re: Question about scaling

Sorry for reposting, but forgot one comment and added it now below: Am 13.11.2012 06:16, schrieb gmx-users-request at gromacs.org: Dear all, i did some scaling tests for a cluster and i'm a little bit clueless about the results. So first the setup: Cluster: Saxonid 6100, Opteron 6272

Re: [gmx-users] Modifying the force field to recognize iron with ligand atoms?

On 11/12/12 9:17 PM, Rajiv Gandhi wrote: Could someone tell how can i modify the specific force field, for example gromacs43a1, to build topology file for protein has iron that interact with some ligands (cytochrome, hemoglobin...etc)? which file i should modify? Heme parameters already

Re: [gmx-users] error : One of the box lengths is smaller than twice the cut-off length

On 11/13/12 3:20 AM, sri2201 wrote: Dear All , I am getting following error while trying the energy minimization by using following command gromacs-4.5.5/proj1% grompp -v -f minim.mdp -c protein-solvated.pdb -p protein.top -o protein-EM-solvated.tpr *ERROR 1 [file protein.top, line 6486]:*

Re: [gmx-users] Re: Question about scaling

Hi, On Nov 13, 2012, at 2:22 PM, Thomas Schlesier schl...@uni-mainz.de wrote: Sorry for reposting, but forgot one comment and added it now below: Am 13.11.2012 06:16, schrieb gmx-users-request at gromacs.org: Dear all, i did some scaling tests for a cluster and i'm a little bit clueless

Re: [gmx-users] Re: error : One of the box lengths is smaller than twice the cut-off length

On 11/13/12 9:05 AM, Dr. Vitaly Chaban wrote: I am getting following error while trying the energy minimization by using following command gromacs-4.5.5/proj1% grompp -v -f minim.mdp -c protein-solvated.pdb -p protein.top -o protein-EM-solvated.tpr *ERROR 1 [file protein.top, line 6486]:*

Re: [gmx-users] position / distance restraint involving more than one molecule

On 11/13/12 9:59 AM, Dr. Vitaly Chaban wrote: Dear All - Is it possible in the current gromacs to apply position restraints NOT in respect to the initial position of the particle, but in respect to an explicitly specified position within a box, such as (0,0,0) or (LBOX/2, LBOX/2, LBOX/2).

[gmx-users] Re: position / distance restraint involving more than one molecule

Thank you, Justin. Supplying desired conf.gro is indeed a wise solution. On Tue, Nov 13, 2012 at 4:02 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/13/12 9:59 AM, Dr. Vitaly Chaban wrote: Dear All - Is it possible in the current gromacs to apply position restraints NOT in respect to the

[gmx-users] Re: Segmentation fault, mdrun_mpi

Hi, I got a similar error for my system: ... [n020110:27321] *** Process received signal *** [n020110:27321] Signal: Segmentation fault (11) [n020110:27321] Signal code: (128) [n020110:27321] Failing at address: (nil) [n020110:27321] [ 0] /lib64/libpthread.so.0 [0x38bac0eb70] [n020110:27321] [ 1]

[gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us

Are there any other tests I should run to diagnose the problem? -- View this message in context: http://gromacs.5086.n6.nabble.com/Diatomic-in-MeCN-NPT-NH-and-PR-simulation-segfaults-after-1-us-tp5001845p5002927.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. --

Re: [gmx-users] calculating lennard-jones interaction

Hi, There is a net attractive force from vdw interactions beyond the cut-off, which can be corrected for analytically *in the case of a homogeneous system*. There is a slight artifact arising from the use of cut-offs for non-homogeneous systems such as a protein in water. Often the same

[gmx-users] Umbrella sampling question

Can you please let us know exactly how you got the two values that you find to be different (but expected to be the same)? i.e. post your full g_dist command and explain how you observed the value in the output from mdrun. One frame should be enough for now (as long as you are sure -- and can

Re: [gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us

On 11/13/12 2:56 PM, benjfitz wrote: Are there any other tests I should run to diagnose the problem? I doubt there's anything that can be done that will be particularly useful. You could compile in debugging mode and try to do a backtrace when the problem occurs, but if you have a means

[gmx-users] Re: hydrophobic contacts

Hi all, can some one tel me how can i prepare a index file specifying the hydrophobic atoms along for measuring the hydrophobic contacts in the systems alone. -- View this message in context: http://gromacs.5086.n6.nabble.com/hydrophobic-contacts-tp4998153p5002931.html Sent from the GROMACS