Re:[gmx-users] Carbohydrate MD Simulation

Hi Nancy, I think that the atom C1 in residue TRP 1 does not exist in rtp entry. In other words, atom C1 is not understood by the software. You should change the atom type in order to be understood. I have a question, how do you obtain the URL about trehalose. Because I want to some polyols

[gmx-users] The difference about NPT and NVT ensemble.

Hello, everyone, I have some questions about ensemble. Would you please tell me about NPT or NVT ensemble? What difference about them? And how to define in the molecular dynamics mdp file? What ensemble does the below parameters extracted from my mdp file? ; Berendsen temperature coupling is

[gmx-users] how to calculate the RMSD of the peptide conformation relative to the NMR structure?

Dear everyone, Can somebody tell me how to calculate the RMSD of the peptide conformation relative to the NMR structure? Thanks again! Fufeng Liu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] How to analyse the number of atom around the protein?

Hi, I am trying to analyse the number of atom around the protein. For example, I want to calculate the number of oxygen atom of water within 3A of the protein. Can somebody tell me how to do it? Or tell me choose which commands to do it. Many thanks in advance, Fufengliu

[gmx-users] How compare the simulated structure of the same peptide to the NMR strucutre?

Hi, all I have simulated a beta-hairpin folded in explicit water, I want to compare the simulated structure to the experimental structure using NMR. Can you tell me how to do it? Thanks a lot! fufengliu ___ gmx-users mailing list

[gmx-users] How to simulate peptide capped with ACE?

Dear gromacs users, I trying to simulate a peptide capped with ACE, when I run grompp, I got the following error: WARNING 1 [file 1.top, line 306]: No default G96Angle types, using zeroes. I checked the topology and found the ACE group disappears. I think that the grompp doesn¡¯t handle

[gmx-users] Error running grompp

Dear gmx users: I m carrying a protein explicit solvent simulation using gromacs 3.3, then i added water, but in next step, I m getting the following error, grompp -f em.mdp -c try.gro -p A.top -o A_em.tpr :-) G R O M A C S (-: Getting the

[gmx-users] Error durign Grompp

Dear gmx users: I m carrying a protein explicit solvent simulation using gromacs 3.3, then i added water, but in next step, I m getting the following error, grompp -f em.mdp -c try.gro -p A.top -o A_em.tpr :-) G R O M A C S (-: Getting the