Re: [gmx-users] the FF parameter sets

Chih-Ying Lin wrote: Hi I think that I did not described my question clearly. #define ga_24 120 505 ; H - N - CH3. H, HC-6-ring, H-NT-CHn 90 three atoms A, B, C form an angle. A-B-C what does this line mean? H - N - CH3. H, HC-6-ring, H-NT-CHn 90 This is a comment line to the pr

Re: [gmx-users] removing degrees of freedome from different proteins at different timesteps of an md simulation

Filip Jagodzinski wrote: > hi gmx-users, > > i haven't been able to accomplish the following: > > i have a system with n atoms, and i want to remove the degrees of > freedom for some of the atoms during different moments of the simulation > > for example, assume the primary sequence of my protei

[gmx-users] removing degrees of freedome from different proteins at different timesteps of an md simulation

hi gmx-users, i haven't been able to accomplish the following: i have a system with n atoms, and i want to remove the degrees of freedom for some of the atoms during different moments of the simulation for example, assume the primary sequence of my protein is a-b-c-d-e-f-g, and, for the firs

[gmx-users] the FF parameter sets

Hi I think that I did not described my question clearly. #define ga_24 120 505 ; H - N - CH3. H, HC-6-ring, H-NT-CHn 90 three atoms A, B, C form an angle. A-B-C what does this line mean? H - N - CH3. H, HC-6-ring, H-NT-CHn 90 does it mean ? =>H - N - CH3 H - N - H, H - N

[gmx-users] RF, was: Re: Gromacs 4.0 beta

Hi David, what is the main problem with RF? Why do you not recommend it? The paper Walser, Hünenberger, et.al., Gargolla Hünenberger et.al. suggest that RF is OK for prot

Re: [gmx-users] which force field for a protein-protein complex?

Ok. I did some "dockings" with know conformation of the protein comlex. The experiment was take the crystallographic complex, obtain the coordinates of each protein in the complex, did the docking experiment to re built the complex, then, take the best complex and to refine it with MD simulation.

Re: [gmx-users] OPLS atom types for THF simulations

On Thu, 2008-09-11 at 14:13 -0300, André Farias de Moura wrote: > Dear Jussi, > try out this one (it works for me) > best regards, > Andre OK, thanks a lot. This cleared up my doubts about which atom types to use, and I was able to get my simulations running. -- --

Re: [gmx-users] OPLS atom types for THF simulations

Dear Jussi, try out this one (it works for me) best regards, Andre ; THF topology - OPLS-AA forcefield [ moleculetype ] ; name nrexcl THF 3 [ atoms ] ; nr type resnr residue atom chgnr 1 opls_1801 THF O1 0 2 opls_1821 THF C2 0 3 op

Re: [gmx-users] S2 order parameters

rams rams wrote: Dear David, I tried to calculate the S2 order parameters using g_rotacf. I removed the rotational and translational degrees of freedom from my trajectory using: trjconv -f -s -o -fit rot_trans Then used this new trajectory to calculate the correlation functions using g_rot

Re: [gmx-users] S2 order parameters

Dear David, I tried to calculate the S2 order parameters using g_rotacf. I removed the rotational and translational degrees of freedom from my trajectory using: trjconv -f -s -o -fit rot_trans Then used this new trajectory to calculate the correlation functions using g_rotacf: g_rotacf -f -s -o

Re: [gmx-users] OPLS atom types for THF simulations

Jussi Lehtola wrote: Hi, I noticed that Jorgensens' group has done tetrahydrofuran (THF) simulations with OPLS-AA. However, I haven't been able to figure out the correct atom types & charges from the GROMACS topology files, by googleing or from Jorgensen's papers. If someone could send me a w

Re: [gmx-users] the FF parameter sets

Chih-Ying Lin wrote: Hi I am looking into the FF parameter sets from the FF.itp. for example #define ga_24 120 505 ; H - N - CH3. H, HC-6-ring, H-NT-CHn 90 I could not understand the last line. Please tell me what it means. ga_XX = Gromos Angle The sets of three atoms ind

[gmx-users] the FF parameter sets

Hi I am looking into the FF parameter sets from the FF.itp. for example #define ga_24 120 505 ; H - N - CH3. H, HC-6-ring, H-NT-CHn 90 I could not understand the last line. Please tell me what it means. Thank you Lin ___ gmx-users mail

[gmx-users] OPLS atom types for THF simulations

Hi, I noticed that Jorgensens' group has done tetrahydrofuran (THF) simulations with OPLS-AA. However, I haven't been able to figure out the correct atom types & charges from the GROMACS topology files, by googleing or from Jorgensen's papers. If someone could send me a working THF OPLS-AA topolo

Re: [gmx-users] Gromacs parellal run:: getting difference in two trajectories

Thanks david for your reply. Can you tell me up to how many -np value current version of GROMACS can be optimized (or will reduce the simulation time) ? Also, how can I test the accuracy of my process when I can't get same result with similar option (while scaling )? With Thanks, Vivek 2008/9/1

Re: [gmx-users] Gromacs parellal run:: getting difference in two trajectories

vivek sharma wrote: Hi There, I am running gromacs parellal version on cluster, with different -np options. Hi, which version of gromacs exactly are you using? On analyzing the 5 nsec trajectory using ngmx, I am finding difference in the trajectory of two similar runs (only thing varying in

Re: [gmx-users] Gromacs parellal run:: getting difference in two trajectories

vivek sharma wrote: Hi There, I am running gromacs parellal version on cluster, with different -np options. On analyzing the 5 nsec trajectory using ngmx, I am finding difference in the trajectory of two similar runs (only thing varying in two runs in -np i.e 20 and 64 ), where mdp file and in

Re: [gmx-users] g_hbond getting abnormal graph

minnale wrote: Thanks Justin for your response you are telling that whatever generated output .xvg files of two systems from g_hbond is perfect. But when I plot .xvg files with help of "xmgrace" it depicting hydrogen bonds represents at bottom and contact pairs above in one plot(one system).

Re: Re: Re: [gmx-users] g_hbond getting abnormal graph

Thanks Justin for your response you are telling that whatever generated output .xvg files of two systems from g_hbond is perfect. But when I plot .xvg files with help of "xmgrace" it depicting hydrogen bonds represents at bottom and contact pairs above in one plot(one system).I am sending file

[gmx-users] Gromacs parellal run:: getting difference in two trajectories

Hi There, I am running gromacs parellal version on cluster, with different -np options. On analyzing the 5 nsec trajectory using ngmx, I am finding difference in the trajectory of two similar runs (only thing varying in two runs in -np i.e 20 and 64 ), where mdp file and input files are same in two

Re: [gmx-users] g_hbond getting abnormal graph

minnale wrote: Hi all, I have issued the command of g_hbond like this g_hbond -f .xtc -s .tpr -n .ndx -num .xvg -hbm.map -a 30 while finishing of this command, it told 1 H-bond found and run successfully. When I plotted .xvg file by using gnuplot its showed zigzag manner graph(abnormal) and

Re: [gmx-users] which force field for a protein-protein complex?

Maximiliano, Could you give some more argumentation regarding your choice of opls-aa? What tests did you use and what were your criteria? Did you verify against experimental data? Paula, I wouldn't go for Gromos 43a1 and most certainly not for ffgmx. The latter is completely obsolete, and the fo

Re: Re: [gmx-users] which "tpr" file to use

 Hi Tsjerk, You have cleared my doubts. I had fitted the structures in the pdb files, which is why I was confused because different coordinates were encountered for the same time step in the original and extended run( that had crashed). Now I understand, where lies the problem.

[gmx-users] g_hbond getting abnormal graph

Hi all, I have issued the command of g_hbond like this g_hbond -f .xtc -s .tpr -n .ndx -num .xvg -hbm.map -a 30 while finishing of this command, it told 1 H-bond found and run successfully. When I plotted .xvg file by using gnuplot its showed zigzag manner graph(abnormal) and I never got this t