[gmx-users] placing dihedral constraints

Hi! I would like to freeze two dihedrals/torsion angles but allow the rest (i.e. bonds, angles) to relax during energy minimization and MD. How do I go over applying constraints? Thanks.-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] placing dihedral constraints

On 06/27/2011 07:31 PM, Mr Bernard Ramos wrote: Hi! I would like to freeze two dihedrals/torsion angles but allow the rest (i.e. bonds, angles) to relax during energy minimization and MD. How do I go over applying constraints? Thanks. See http://www.gromacs.org/Documentation/Terminology/C

[gmx-users] missing topology file adn creating a new one

Dear all, i am doing a sampling method and in a stage of completion But unfortunatelymy topol.top file is missing and am really helpless .i cant continue the simulation.i have the tpr file adn pdb file at last step.i tried to create the top file from *g_x2top -f beta_md17.tpr -o topo

Re: [gmx-users] missing topology file adn creating a new one

sreelakshmi ramesh wrote: Dear all, i am doing a sampling method and in a stage of completion But unfortunatelymy topol.top file is missing and am really helpless .i cant continue the simulation.i have the tpr file adn pdb file at last step.i tried to create the top file from

Re: [gmx-users] Periodic Images - clarification

Dear Sir Thanks I got the point! Thanking you With Regards M. Kavyashree On Mon, Jun 27, 2011 at 12:19 PM, Tsjerk Wassenaar wrote: > Hi Kavya, > > > I did use dodecahedron cell. but how does using a dodecahedron cell > > be advantageous than any other cell when minimum image violation > > has

[gmx-users] g_msd bug

Hi GMX Users, I am writting this email, beacause I think the g_msd program in Gromacs 4.5.4 bears a problem. I was calculating the MSD od center of mass of POPC in membrane (system contains 274 POPC lipid molecules in all-atom force field) from 50 ns trajectory and it seems to consume great amou

Re: [gmx-users] g_msd bug

Hi Slawomir, That's quite a usage of memory! Can you provide more information? Like the number of frames in the trajectory, the command line you used, and the system you ran on? Cheers, Tsjerk 2011/6/27 Sławomir Stachura : > Hi GMX Users, > I am writting this email, beacause I think the g_msd p

[gmx-users] Comparing MD ensembles with exp. NOE restraints --> bus error

Hi There, I would like to compare my ensemble of (unrestrained) MD structures against experimental NOE distances. For that, I have added the distance_restraints block to my *.top file such as: [distance_restraints] ;aiaj type index type’ low up1 up2 fac 3331101 0.0 3.00

Re: [gmx-users] Comparing MD ensembles with exp. NOE restraints --> bus error

Thereza Soares wrote: Hi There, I would like to compare my ensemble of (unrestrained) MD structures against experimental NOE distances. For that, I have added the distance_restraints block to my *.top file such as: [distance_restraints] > ;aiaj type index type’ low up1 up2 fac > 33

Re: [gmx-users] g_msd bug

Hello, thank you for your reply. I have used following command : g_msd -n POPC.ndx -lateral z -o POPC_msd.xvg -mol POPC_diff.xvg Trajectory has 1 frames and the system it was ran on is Fedora Red Hat 5.4. Indeed my network administrator was very unhappy about comsumed memory. Regards,

[gmx-users] about periodic images violation

Dear gmx-users, I'm inserting into the discussion about periodic images since I'm experimenting a problem of minimum distance violation too. I'm doing simulations on a dimeric protein (with no covalent bonds between the two subunits) which derives not from a crystallographic structure but from a mo

[gmx-users] Regarding NPT Eq.

Dear All, I have been trying to do NPT equilibration for 100 ps. I have tried with different tau_p like from 0.5 to 2 and my reference pressure is 1 bar. Since I am continuing from 20 ps NVT equilibrated configuration, in npt.mdp I have written init_step = 1 (1*0.02 fs = 20 ps). But instea

Re: [gmx-users] about periodic images violation

Hi Anna, The spikes you see occur because the protein is broken over the periodic boundaries. Not hard to see that a broken molecule will have a minimal minimal distance. The other problem may well occur due to rotation of your molecule. Since you set -bt tric, you just get a rectangular unit cel

[gmx-users] g_msd bug

600 GB of memory? I highly doubt that you have that much memory available. Are you sure that this is not a typo? Can you please post evidence that you have >=600 GB of memory available? It is common for clusters to disallow an individual process from using >10% of the total memory on a head

Re: [gmx-users] Regarding NPT Eq.

Hi What do you mean with "not being able to equilibrate to 1 bar"? Could you please post g_energy output and which pressure coupling scheme are you using? Keep in mind that pressure suffers from large oscillations (http://www.gromacs.org/Documentation/Terminology/Pressure). Also, depending on

[gmx-users] minimization problem (Martini simulation)

Dear Gromacs users and developers, I forgot to note that I'm talking about a Martini simulation. I'm trying to set up simulation. I have a big simulation of something like half million CG atoms. The problem is that I have a minimization problem. I'm getting the following error: Converged to m

[gmx-users] minimization problem

Dear Gromacs users and developers, I'm trying to set up simulation. I have a big simulation of something like half million atoms. The problem is that I have a minimization problem. I'm getting the following error: Converged to machine precision, but not to the requested precision Fmax < 10 I

Re: [gmx-users] g_msd bug

No -it is not a typo - my cluster allows me to use higher amount of memory than 10%. Information I received from administrator of the cluster : >> [root@isei ~]#top >> >> top - 13:52:23 up 30 days, 3:00, 76 users, load average: 5.85, 17.19, >> 13.08 >> Tasks: 2825 total, 1 running, 2815 sleep

Re: [gmx-users] minimization problem (Martini simulation)

pol...@fh.huji.ac.il wrote: Dear Gromacs users and developers, I forgot to note that I'm talking about a Martini simulation. I'm trying to set up simulation. I have a big simulation of something like half million CG atoms. The problem is that I have a minimization problem. I'm getting the fol

[gmx-users] Re: gmx-users Digest, Vol 86, Issue 183

Hi Justin, I have used the same files to re-run using gromacs-4.5.4 and the only difference is that I get a "segmentation fault" instead of "bus error" message. Thanks for your help, I will then fill out the issue report as you suggested. Best, Thereza Professor Thereza A. Soares Departamento

[gmx-users] g_covar : segmentation fault

Hi, I am doing Dihedral PCA and followed the steps as mentioned in the Gromacs documentation http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA Below are the commands i used: 1) I generated index file for chosen dihedral angles. 2) g_angle -f 100ns_noPBC.xtc -n dangle.ndx -or dangle.tr

Re: [gmx-users] g_covar : segmentation fault

Poojari, Chetan wrote: Hi, I am doing Dihedral PCA and followed the steps as mentioned in the Gromacs documentation http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA Below are the commands i used: 1) I generated index file for chosen dihedral angles. 2) g_angle -f 100ns_noPBC.xtc

[gmx-users] The RMSD of a metal ion

Hi, I would like to look at the positions of a metal ion in MD relative to its original crystal position. I tried g_rms, and I got the following message: "Fatal error : Need >= 3 points to fit" Did I use the correct command to achieve this task? Thanks for your insight in advance. Simon -- g

Re: [gmx-users] The RMSD of a metal ion

simon sham wrote: Hi, I would like to look at the positions of a metal ion in MD relative to its original crystal position. I tried g_rms, and I got the following message: "Fatal error : Need >= 3 points to fit" Did I use the correct command to achieve this task? Generally, when one rec

Re: [gmx-users] minimization problem (Martini simulation)

Dear Justin, Thank you very much for your answer. Can you please explain me what do you mean by saying "EM wasn't sufficient". What information do you need in order be able to help? I run EM with emtol=60 and I got the following energies: Steepest Descents converged to Fmax < 60 in 2256 steps P

Re: [gmx-users] minimization problem (Martini simulation)

pol...@fh.huji.ac.il wrote: Dear Justin, Thank you very much for your answer. Can you please explain me what do you mean by saying "EM wasn't sufficient". What information do you need in order be able to help? I run EM with emtol=60 and I got the following energies: Steepest Descents converge

[gmx-users] pull direction of steered MD in Gromacs

Dear Gromacs Users, Can you assign any pulling direction in Gromacs rather than only using the axial x/y/z direction? pull_dim= N N Y Can we assign sth. like a vector in gromacs? Thanks, Tom -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

Re: [gmx-users] pull direction of steered MD in Gromacs

Tom wrote: Dear Gromacs Users, Can you assign any pulling direction in Gromacs rather than only using the axial x/y/z direction? pull_dim= N N Y Can we assign sth. like a vector in gromacs? Yes, see the pull_vec option and other related topics in the pulling tutorial: http://ww

Re: [gmx-users] g_msd bug

On 27/06/2011 11:57 PM, Sławomir Stachura wrote: Hello, thank you for your reply. I have used following command : g_msd -n POPC.ndx -lateral z -o POPC_msd.xvg -mol POPC_diff.xvg Trajectory has 1 frames and the system it was ran on is Fedora Red Hat 5.4. Indeed my network administrator was

Re: [gmx-users] plateau in msd (glass transition); ref_t

On Jun 23, 2011, at 5:07 AM, Anja Kuhnhold wrote: > I'm simulating a bead-spring polymer model (1600 chains and 10 beads per > chain in a 26.6^3 box with pbc) with LJ and FENE potentials. > I calculate the mean-square-displacement for different temperatures. For > T=0.46 (in LJ units) I expected