Re: [gmx-users] DNA-protein complex

The force field that I used was ambe99bsc0, and my input file was: ; 7.3.3 Run Control integrator = md; md integrator tinit = 0 ; [ps] starting time for run dt = 0.002 ; [ps] time step for

[gmx-users] comparison of entropy and enthalpy at different temperatures

Hi, I'll be happy if some one can help. I have a large system containing of 17000 water molecules and 1000 lutidine molecules. I am simulating the mixture at different temperatures, T, close to the mixture's critical point. I want to investigate competition between entropy and enthalpy at

Re: [gmx-users] A jump in potential just after extension

Dear Justin, I use gromacs/4.6.7. http://4.6.0.7/ Below is my .mdp file. No that is not similar to my case, I do not change any setting for the extension. (I should add that despite strange jump in potential in g_energy, the trajectory goes in a direction which I expect.)

Re: [gmx-users] DNA-protein complex

2015-03-18 5:26 GMT-03:00 Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl: The force field that I used was ambe99bsc0, and my input file was: ; 7.3.3 Run Control integrator = md; md integrator tinit = 0 ; [ps]

Re: [gmx-users] jump problem

On 3/17/15 9:03 PM, Ahmet yıldırım wrote: Dear users, I tried to remove the jumps of a structure after simulation but I couldn't do it. The structure is heterodimer. I tried the following ways: 1) -gmx trjconv -f md.xtc -s md.tpr -o traj_nojump.xtc -pbc nojump -gmx trjconv -f traj_nojump.xtc

Re: [gmx-users] jump problem

Hey :) Cluster the first frame and write out as new reference structure. Then run with that reference, removing jumps. Cheers, Tsjerk On Mar 18, 2015 12:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/17/15 9:03 PM, Ahmet yıldırım wrote: Dear users, I tried to remove the jumps of a

Re: [gmx-users] DNA-protein complex

On 3/18/15 4:26 AM, Urszula Uciechowska wrote: The force field that I used was ambe99bsc0, and my input file was: What is the DNA sequence? We have seen some cases where AMBER99-parmbsc0 fails to capture global characteristics of DNA structure. This is a common problem among additive

Re: [gmx-users] umbrella sampling tutorial

On 3/17/15 9:06 PM, Ming Tang wrote: Hi Justin, Thanks a lot. I can move forward now. Recently, I am trying to pull a triple helix, and want to fix the center of mass of the three terminal atoms. One paper said that it can be done by means of a strong harmonic restrain with a super large

[gmx-users] PDB for nafion

Dear all, I want to simulate nafion oligomers in explicit water. Is there any tool or any software where I can build a short nafion residue? How consistent will be the bond length/angle parameters with respect to the employed force field? I am quite new in the filed of molecular

[gmx-users] error while equilibration

I am trying to simulate RNA in water. I have minimized the system with steepest Decent for 2000 steps and then with Conjugate gradient for till the energy coverage reaches to 100 Kj/mol. But when I am trying to equilibrate it I am getting following error

Re: [gmx-users] error while equilibration

On 3/18/15 12:01 PM, ananyachatterjee wrote: I am trying to simulate RNA in water. I have minimized the system with steepest Decent for 2000 steps and then with Conjugate gradient for till the energy coverage reaches to 100 Kj/mol. But when I am trying to equilibrate it I am getting following

Re: [gmx-users] Error while shrinking lipids (KALP15 in DPPC tutorial)

On 3/18/15 4:05 PM, Thomas Lipscomb wrote: Dear gmx-users, This means someone has removed gb.itp from the charmm36.ff directory and hence grompp fails. If someone has been toying with the contents of the force field, start fresh with a new tarball from:

[gmx-users] potential energy is from energy mimization

Dear gmx, I am simulation a kinase protein which has (~1200 aa) length. When I energy minimize the protein with default em file from Justin A. Lemku tutorial. i have got the following output. writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 1162 steps

[gmx-users] Core Dump

Hi All, I am using GRMACS 5.0.4, I got and error: Core dump on signal SIGBUS (7) suppressed. There was a warning: This run will generate roughly 3298 Mb of data. Kind regards, Alex -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Core Dump

Hi, Thanks for help. It was not grommp fault. The command line was mdrun_mpi -ntomp 1 -s relaxation.tp -deffnm relaxation -c HAP_relaxation.pdb Hope following can help. MPT: On host cl2n109, Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 0, Process 220661: Dumping core on signal SIGBUS(7)

[gmx-users] How to set a system consists of membranes and cholestrols

Dear gmx_users, Hello, I want to simulate membrane system that contains lipids, cholestrols and glycolipids. Is there any suggestions, advice and some useful links? Best regards, Batsaikhan -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Core Dump

On 3/18/15 7:48 PM, BAOLIN HUANG wrote: Hi All, I am using GRMACS 5.0.4, I got and error: Core dump on signal SIGBUS (7) suppressed. There was a warning: This run will generate roughly 3298 Mb of data. So grompp seg faults? You're going to have to provide real information, like what

[gmx-users] changing partial charge/atom type upon covalent bonding

Dear users, I need to simulate a protein which is covalently bonded to some covalent inhibitors using GROMACS 5.0.4 and the AMBER99SB-ILDN force field. Thanks to the user discussion list I successfully used specbond.dat and suitable modifications in a local copy of the forcefield to

Re: [gmx-users] potential energy is from energy mimization

On 3/18/15 9:42 PM, Rj wrote: Dear gmx, I am simulation a kinase protein which has (~1200 aa) length. When I energy minimize the protein with default em file from Justin A. Lemku tutorial. i have got the following output. writing lowest energy coordinates. Steepest Descents converged

Re: [gmx-users] Core Dump

On 3/18/15 8:51 PM, BAOLIN HUANG wrote: Hi, Thanks for help. It was not grommp fault. The command line was mdrun_mpi -ntomp 1 -s relaxation.tp -deffnm relaxation -c HAP_relaxation.pdb Hope following can help. MPT: On host cl2n109, Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 0,

[gmx-users] pdb2gmx error

Dear gmx, I tried to to use pdb2gmx and get this error for 3 to 4 residues. I even cleaned my crystal structure using Discovery studio/swissviewer which shows no error on it. I wonder, how do i rectify this problem ? WARNING: WARNING: Residue 1 named MET of a molecule in the input file was

[gmx-users] Membrane simulation

Hi,I want to simulate membrane system that contains lipids, cholesterol and glycolipid. Is it possible to simulate entire membrane structure. Kindle help me to simulate such system.Thank you, With Regards, A.Petrishia Department of ECE, College of Engineering,Guindy, Anna University,

Re: [gmx-users] g_dist

hello everyone i am unable to understand the result of gmx check .it gives frames and time values .g_dist is worked in all protein related residues but i want to calculate the distance between some residues of protein and ligand for ligand i got same problem like mismatch. kindly help On Mon,

[gmx-users] Tutorial For Installing Gromacs on window

Greetings, I want to install gromacs on window 7. but i don't know the exact procedure.could you please explain me the procedure to install gromacs on window. Thanking you in anticipation -- Gromacs Users mailing list * Please search the archive at

[gmx-users] distribution of water molecules

Dear all, I have a box of water molecules and a peptite amphiphile based cylindirical nanofiber. I would like to find the density distribution of water. To do this: 1) I created an index file which contains OW atoms (=Oxygen atoms that belong to the water molecules) 2) Then, I used the

Re: [gmx-users] Error while shrinking lipids (KALP15 in DPPC tutorial)

Dear gmx-users, This means someone has removed gb.itp from the charmm36.ff directory and hence grompp fails.  If someone has been toying with the contents of the force field, start fresh with a new tarball from: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. -Justin Thanks.