Re: [gmx-users] a residue move in extremely large scale in MD

Dear Catch ya,   I have watched the trajectory of the simulation. Besdies, I got the PDb file for the whole 10 ns MD every 500 ps. Then I compared all the PDB files generated, and it confirms that 1 specific residues moves in an extremely large space.   Can you give me an explaination on it?  

[gmx-users] Question about Thermodynamic Integration

Dear Gromacs users Hi. I wanted to ask about the use of Thermodynamic Integration. If the two compared molecules have a different number of atoms (e.g Theophylline and Methylxanithe) what should I do in order to simulate it well (it's written that you have to have the same number of atoms)?

[gmx-users] Abnormal alignment of waters after NVT simulation

Dear All, I encountered a very weird result after performing NVT simulation, all the waters aligned in lines, and they look like crystal cells. How did it turn out like this by temperature coupling? The following is the nvt.mdp parameters: ; NVT equilibration define = -DPOSRES

Re: [gmx-users] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...

Hi Gromacs Friends, After your reply, Itried in another way . I install the openmpi and fftw3 to the /opt/.. at the time of make (for gromacs) I encouner with error suggesting to recompile with -fPIC.. As per instruction in website, I added glag --enable-shared to the fftw, but again at the

AW: [gmx-users] a residue move in extremely large scale in MD

That's hard to judge for everyone but you, because there are too many questions left. What kind of residue is it? Is it at one of the protein termini, is it on the surface or buried by other sections? Are there interactions with other parts of the system? Did you check the RMSD or RMSF-values

[gmx-users] What 's the format of tabble for dihedral potential ?

Dear all, In MD silulation, usually we use the  default function type for the dihedral potential. For example, type 3 means the Ryckaert-Bellemans function. However, sometimes we meet with some strange dihedrals that cannot be fitted by these functions, in this way we choose the tabulate

Re: [gmx-users] Question about Thermodynamic Integration

you have to run 10X times with different random seeds to confirm your results. Most importantly, you have to do biochemistry mutagenis to fully support your hypothesis otherwise nobody will believe your theoretical results good luck On 08/08/2012 09:11 AM, Asaf Farhi wrote: Dear Gromacs

Re: [gmx-users] Error in ligand coordinate file

Hi justin, Thanks for reply now i have ligand corrdinate file as follows ATOM 1 N A -13.006 -12.965 -0.251 -0.60 -0.09 N ATOM 2 C A -13.386 -13.020 1.035 -0.38 0.03 C ATOM 3 C A -13.037 -14.131 1.869 -0.32 -0.03

Re: [gmx-users] Question about Thermodynamic Integration

On 8/8/12 3:11 AM, Asaf Farhi wrote: Dear Gromacs users Hi. I wanted to ask about the use of Thermodynamic Integration. If the two compared molecules have a different number of atoms (e.g Theophylline and Methylxanithe) what should I do in order to simulate it well (it's written that you

Re: [gmx-users] Error in ligand coordinate file

On 8/8/12 5:37 AM, sai nitin wrote: Hi justin, Thanks for reply now i have ligand corrdinate file as follows ATOM 1 N A -13.006 -12.965 -0.251 -0.60 -0.09 N ATOM 2 C A -13.386 -13.020 1.035 -0.38 0.03 C ATOM 3 C A

RE: [gmx-users] Question about Thermodynamic Integration

Dear Justin Thank you very much for the reply. It's written in the manual: 5.7.4 Topologies for free energy calculations Free energy differences between two systems, A and B, can be calculated as described in sec. 3.12. Systems A and B are described by topologies consisting of the same number

RE: [gmx-users] Question about Thermodynamic Integration

This is why I still don't understand. Best regards, Asaf From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Asaf Farhi [asaf.fa...@weizmann.ac.il] Sent: Wednesday, August 08, 2012 1:35 PM To: Discussion list for GROMACS users

[gmx-users] Gromacs to AMBER

Hi all, Can any body know how to take Gromacs trajectories of protein ligand system to AMBER MM-PBSA and further calculate binding free energies using MM-PBSA.. Can any body suggest some tutorials..on this Cheers -- Sainitin D -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Error in ligand coordinate file

Hi justin, Ok i will explain more clearly what i really have is protein ligand complex from Autodock..I choose best complex based on predicted binding affinity. Using pymol i visualized complex.pdb and saved only ligand (ligand.pdb given below) and used swiss param tool online

Re: [gmx-users] Question about Thermodynamic Integration

On 8/8/12 6:35 AM, Asaf Farhi wrote: Dear Justin Thank you very much for the reply. It's written in the manual: 5.7.4 Topologies for free energy calculations Free energy differences between two systems, A and B, can be calculated as described in sec. 3.12. Systems A and B are described by

Re: [gmx-users] Error in ligand coordinate file

On 8/8/12 10:44 AM, sai nitin wrote: Hi justin, Ok i will explain more clearly what i really have is protein ligand complex from Autodock..I choose best complex based on predicted binding affinity. Using pymol i visualized complex.pdb and saved only ligand (ligand.pdb given below) and used

RE: [gmx-users] Question about Thermodynamic Integration

Dear Justin Thank you very much for the reply. I want to understand how to calculate binding free energy difference of both molecules to another molecule. So do I have to use dummy atoms, meaning that there won't other forces besides the bonding term? I'll look at the examples. Thanks, Best

RE: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

Thanks for the suggestion. I tried it, but for my system the gain is not significant.  I was aware that it is preferable to remove the centre-of-mass for each leaflet separately. However, in my tests, I removed the center-of-mass of the membrane because I intent to simulate peptide-membrane

Re: [gmx-users] Question about Thermodynamic Integration

On 8/8/12 11:25 AM, Asaf Farhi wrote: Dear Justin Thank you very much for the reply. I want to understand how to calculate binding free energy difference of both molecules to another molecule. So do I have to use dummy atoms, meaning that there won't other forces besides the bonding term?

[gmx-users] add a new bond to a force field

Dear gmx friends, I'm supposed to add a bond not defined in bond-types by default. I used cgenff and got the bond parameters as this: CG2O1  HGR52   317.13 1.1000 ! FORM, formamide reverted to value from par_all22_prot.inp and par_cgenff_1d.inp I know the atomtypes are not in agreement,

Re: [gmx-users] add a new bond to a force field

On 8/8/12 2:58 PM, Shima Arasteh wrote: Dear gmx friends, I'm supposed to add a bond not defined in bond-types by default. I used cgenff and got the bond parameters as this: CG2O1 HGR52 317.13 1.1000 ! FORM, formamide reverted to value from par_all22_prot.inp and par_cgenff_1d.inp

RE: [gmx-users] a residue move in extremely large scale in MD

No, I can't, since you are the one with all the information in front of you, and I only have a couple of sentences filtered through you on what is going on. Some questions you can ask yourself to help answer the question you have: And what did the residue do while you watched the

Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

On 9/08/2012 3:28 AM, Sebastien Cote wrote: Thanks for the suggestion. I tried it, but for my system the gain is not significant. I was aware that it is preferable to remove the centre-of-mass for each leaflet separately. However, in my tests, I removed the center-of-mass of the membrane

Re: [gmx-users] Abnormal alignment of waters after NVT simulation

On 8/08/2012 5:58 PM, Du Jiangfeng (BIOCH) wrote: Dear All, I encountered a very weird result after performing NVT simulation, all the waters aligned in lines, and they look like crystal cells. If they're in geometric lines, then you're probably looking at your input configuration. If

Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

Personally, I could remove the COM of each leaflet when equilibrating the bilayer by itself (and as a side note I am not experiencing a similar problem with POPC that you're having with POPE...). However, after the protein is embedded, I have gotten good results for my protein, which extends from

[gmx-users] mdrun-gpu

Dear Gromacs Users, I am trying Gromacs/4.5.5-OpenMM on GPU with CUDA support. when I run grompp-gpu to generate the .tpr file, it worked well: grompp-gpu -f input_min.mdp -o min.tpr -c box1.g96 however, then I run mdrun-gpu mdrun-gpu -s min -o min -c min.g96 -x min -e min -g min, it was stopped