[gmx-users] Box size to be considered in editconf

Dear all, What should be the size of a cubic box in the command editconf for simulating a protein-protein complex consisting of 500 residues altogether? Thanks in advance. -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 169, Issue 67

On 5/18/18 12:39 PM, SHYANTANI MAITI wrote: > Dear all, > What should be the value of d in editconf command for a protein-protein > complex of 500residues and length of protein is 6.5nm maximum. > I have simulated it using the command: > editconf -f conf.gro -bt cubic

[gmx-users] Box size to be considered for a protein of length 500 residues and dimension of protein is 6.5nm maximum.

as 1and d as 6, I find that the protein is solvated properly in both cases. Can I consider the value of d as 1 instead of 6 for my specified protein-protein complex? Thank you, -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

[gmx-users] Protein protein complex simulation to be done with respect to observe changes in temperature

the final md simulation? Thanks in advance, -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un

[gmx-users] Equilibration step in MD

Dear all, The rmsd obtained after equilibration of protein-protein complex at 1atm pressure is quite high(5times) but the rmsd obtained for only 100ps simulatrion of equilibration is quite stable. Which rmsd should be considered? -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue 139

nriques) >2. Re: Number of Xeon cores per GTX 1080Ti (Mark Abraham) >3. mdrun on single node with GPU (Myunggi Yi) >4. RMSD values consideration (SHYANTANI MAITI) >5. Re: RMSD values consideration (Ahmed Mashaly) > > > -

[gmx-users] Protein protein complex md simulaton

Dear all, Does there exist any differences between the steps to follow for protein and protein-protein complex md simulation? -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] Protein protein complex molecular dynamic simulation

Can molecular dynamic simulation be performed over protein-protein complexes using gromacs? Thanking you, -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post

[gmx-users] Potential energy coming out to be zero but not negative

equilibration or do I need to obtain only negative energy and after that only should I start my equilibration? Does the value of potential energy obtained after minimization need to be negative in all cases? Can I continue my equilibration with this result? Thanking you -- Best regards, *Shyantani Maiti

[gmx-users] Convergence of system

from covar function of gromacs. How can I understand the convergence of system from the correlation function? -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post

[gmx-users] Format of xvg file

other frames are missing..can you please suggest the exact file format of xvg file to compute time correlation function? -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can'

[gmx-users] Reaching equilibrium

Dear all, How to understand whether a system(large system) reaches equilibrium after MD simulation? -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] Convergence of system

created from covar function of gromacs. How can I understand the convergence of system from the correlation function? -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

[gmx-users] Convergence of system

created from covar function of gromacs. How can I understand the convergence of system from the correlation function? Thanking you -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] Convergence of systems.

Dear all, How to determine whether the system converges or not in molecular dynamics simulation? -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] Sudden increase in RMSD values for 100ns simulation of protein-protein complex

of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity generation is off -- Best regards, *Shyantani Maiti* -- Gromacs Users

[gmx-users] Sudden increase in RMSD values for 100ns simulation of protein-protein complex

? -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https

[gmx-users] RMSD values consideration

I use this result for my analysis? Is the rmsd correctly obtained? -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support