How do I do PCA for Protein bound sam with RNA Complex (3system) After doing PCA , I WANT to have a look on the animation of pca1 but the problem is that RNA is broken and SAM is also broken . sometimes , IT is flying away . How to do pca of this three complex properly ?? HELPPPPP GROMACS version: GROMACS modification: Yes/No Here post your question 1 post - 1 par…

GROMACS version: 2021.2 GROMACS modification: No Hi, I am new to GROMACS and I ran into some problems. So far I’ve been able to simulate the dynamics of our enzyme of interest in an aqueous solution. Now I wanted to add 1M trehalose to the system and compare how it affects the natural structure of the protein. Could anyone guide me a little bit on how I should do this? Thanks…

GROMACS version: 2021.4 GROMACS modification: Yes/No Here post your question I want to measure the IFT between oil and water. At first I ran the simulation with a mixture of hydrocarbons (representing the oil phase) in water at 298 K in an NVT run for 20 ns. Herein, the oil formed a ball surrounded by water. Now, in order to determine the IFT value I have to run an NPAT simulati…

GROMACS version: GROMACS modification: Yes/No Here post your question For this i use the command gmx make_ndx -f md_0_150.gro -o dist.ndx and make a index file for the atoms of my choice Available static index groups: Group 0 “r_6_&O1P" (1 atoms) Group 1 "r_14&O4’" (1 atoms) Group 2 “r_13” (32 atoms) Group 3 "r_13&H3" (1 atoms) Group 4 "r_12&H42" (1 a…

Dear users, I use 4.6.5 Gromacs. I have simulated dppc bilayer lipid and for the md part, I used grompp like below: grompp -f md.mdp -c dppcnpt.gro -p topol.top -maxwarn 10 mdrun -v -c dppcmd.gro in this way, md.tpr and md.xtc aren’t made. but for analyzing my bilayer I need both of these files. so I wrote trjconv -f traj.trr -o md.tpr but when I wanted to index some ato…

GROMACS version: 2021.3 GROMACS modification: Yes Hi, I added an extenal potential to the force field but it seems that the simulation is not stable. Since the h-bonds are constrained but the external potential have additional forces on hydrogens, there are some LINCS warnings: Step 140957, time 281.914 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 3.462…