Re: [gmx-users] Question about cut-off values with respect to the neighbor list

On 8/18/12 5:59 PM, Andrew DeYoung wrote: Hi, If you have time, I have some questions about the neighbor list and cut-off values. I am running NVT simulations with coulombtype = PME and vdwtype = cut-off. I have specified equal neighbor search, vdw, and Coulomb cut-offs: rlist = 1.5 nm, rvdw

Re: [gmx-users] KALP15 In DPPC

On 8/18/12 6:20 PM, Shima Arasteh wrote: Dear all, I'm doing the protein-lipid membrane simulation by Justin's tutorial of KALP15 in DPPC. I modified the force field as said in tutorial. Next in grompp step I get a warning as below: WARNING 1 [file ffnonbonded.itp, line 3097]: Overriding

Re: [gmx-users] 2 chain protein and VMD

On 19/08/2012 10:12 AM, Acoot Brett wrote: Dear Rui and All, For the initial PDB file for my MD, it contains chain A (residue 1-400) and B (residue 1-40). After I load the trajectory file to VMD, I find it has converted both chain A and B to chain X. And in chain X it contains the original seq

Re: [gmx-users] 2 chain protein and VMD

Dear Rui and All,   For the initial PDB file for my MD, it contains chain A (residue 1-400) and B (residue 1-40). After I load the trajectory file to VMD, I find it has converted both chain A and B to chain X. And in chain X it contains the original sequences of both chain A and chain B, which m

[gmx-users] KALP15 In DPPC

Dear all, I'm doing the protein-lipid membrane simulation by Justin's tutorial of KALP15 in DPPC. I modified the force field as said in tutorial. Next in grompp step I get a warning as below: WARNING 1 [file ffnonbonded.itp, line 3097]:   Overriding LJ-14 parameters.   old: 0.00261735 2.63413e-

[gmx-users] Question about cut-off values with respect to the neighbor list

Hi, If you have time, I have some questions about the neighbor list and cut-off values. I am running NVT simulations with coulombtype = PME and vdwtype = cut-off. I have specified equal neighbor search, vdw, and Coulomb cut-offs: rlist = 1.5 nm, rvdw = 1.5 nm, rcoulomb = 1.5 nm. Is it a good id

[gmx-users] structure factor

Dear gmx users. I am new for MD and am learning hard but need to ask simple question,,, I have co2 + water system. I understand RDF and it can calculate with g_rdf by choosing 2 species like o-o, c-o, etc. I also want to learn structure factor. But for structure factor can only choose 1 species,

RE: [gmx-users] 2 chain protein and VMD

Hi, You could do something like this: set sel1 [atomselect top "residue 0 to 499"] $sel1 set chain A set sel2 [atomselect top "residue 500 to 999"] $sel2 set chain B Hope this helps, Rui Rodrigues De: gmx-users-boun...@gromacs.org [gmx-users-boun...@gro

[gmx-users] 2 chain protein and VMD

    Dear All,   After the production MD for a 2-chain protein complex (chain A and chain B) was done, I used VMD to observe the trajectory. I want to color the 2 chains in different color.   However it seems during the observation of the trajectory by VMD, VMD treated both of the 2 chains as ch