Re: [gmx-users] unusual bonds

Hi Mark, Thanks for your reply! Sudip On Mon, Feb 8, 2016 at 12:49 PM, Mark Abraham wrote: > Hi, > > This is normal. Remember that vmd didn't read your topology file, it read a > different .gro file each time and made different guesses about where bonds > might be.

Re: [gmx-users] fixing PBC view

Thanks a lot for your help! Indeed it works for me. On Sun, Feb 7, 2016 at 9:14 PM, Justin Lemkul wrote: > > > On 2/7/16 7:48 AM, Netaly Khazanov wrote: > >> Hi All, >> My system is including the small compound with penetrates the membrane >> lipids. I've ran the MD simulation

Re: [gmx-users] pp/pme ratio differences between gromacs 5.0.x and 5.1.x

Hi, you could try to manually set the number of PME nodes with -npme in 5.1. Does that reproduce the 5.0 performance? Carsten > On 07 Feb 2016, at 19:57, Johannes Wagner wrote: > > hey guys, > came across an issue with pp/pme ratio difference from 5.0 to 5.1. For a

[gmx-users] Equilibration error

Hi gromacs users, I have found error in equalibration step  in my simulation. Kindly give your valuable suggestions. Fatal error: 2 particles communicated to PME rank 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually

Re: [gmx-users] Equilibration error

On 2/8/16 5:22 AM, Abid Channa wrote: Hi gromacs users, I have found error in equalibration step in my simulation. Kindly give your valuable suggestions. Fatal error: 2 particles communicated to PME rank 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their

Re: [gmx-users] fatal error.Atomtype LC3 not found.

On 2/8/16 12:09 AM, Waqas khan wrote: Dear gromacs expert ! I want to insert the GPCR protein in POPC bilayer but getting fatal error. I am using Charrm36 force field. I am new to MD simulation. *Fatal error:Atomtype LC3 not foundFor more information and tips for troubleshooting, please

Re: [gmx-users] topology and coordinate file not matching after grompp

Dear Swagata, You have to include the benzene molecules in your topology section. [ molecules ] ; Compound#mols Protein_chain_A 1 PDB 250*6 SOL 7217 BENZENE xyz It should solve your problem. Sapna. Sapna Mayuri Borah c/o Dr. A. N. Jha

[gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

Dear all, I have tried running the same protein in the two versions of gromacs 4.6.5 and 5.0.4. Now, both the runs are producing entirely different results. The results till equilibration are same. After the run however, there is a total change in the production results. I have used the same

Re: [gmx-users] topology and coordinate file not matching after grompp

Hi Swagata, You can't use expressions: 250*6 Cheers, Tsjerk On Feb 9, 2016 06:34, "Swagata Patra" wrote: > Dear Sapna. > > After adding benzene molecules also I am getting the same error. > > On Tue, Feb 9, 2016 at 10:56 AM, SAPNA BORAH > wrote:

Re: [gmx-users] topology and coordinate file not matching after grompp

Dear Sapna. After adding benzene molecules also I am getting the same error. On Tue, Feb 9, 2016 at 10:56 AM, SAPNA BORAH wrote: > Dear Swagata, > > You have to include the benzene molecules in your topology section. > > [ molecules ] > > ; Compound#mols > >

Re: [gmx-users] DMF molecule

On 09/02/16 06:37, mohammad r wrote: Hi everybody, I have the DMF pdb file and I want to import it to gromacs by pdb2gmx command, but the residues are not included in none of the forcefields. can you please help me figure this out? Thank you, Mohammad. Maybe this one?

Re: [gmx-users] creating representative structures

Hi, On Mon, Feb 8, 2016 at 6:24 PM Shyno Mathew wrote: > Dear all, > > > I have few questions regarding creating representative structures. For > simplicity, let’s say I have a trajectory of 5 frames: > > 1. g_rmsf: After reading previous posts, here is what I

[gmx-users] topology and coordinate file not matching after grompp

Hi gromacs users. I am trying to simulate a protein is mixed solution of water and 25% benzene using gromos force field. I tried to follow the steps suggested on gromacs website. Here are the commands that I used: > pdb2gmx_d -f protein.pdb -o protein_processed.gro -water spce -ignh >

[gmx-users] DMF molecule

Hi everybody, I have the DMF pdb file and I want to import it to gromacs by pdb2gmx command, but the residues are not included in none of the forcefields. can you please help me figure this out? Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

Hi, This is quite normal. http://www.gromacs.org/Documentation/Terminology/Reproducibility. You should see a similar range of variation in the trajectories produced in the two versions that are incompletely sampling the same ensemble, but one can say very little about two single observed

[gmx-users] topology and coordinate file not matching after grompp

Hi gromacs users. I am trying to simulate a protein is mixed solution of water and 25% benzene using gromos force field. I tried to follow the steps suggested on gromacs website, which are: 1‐ Determine the number of co‐solvent molecules necessary, given the box dimensions of your system. 2‐

Re: [gmx-users] topology and coordinate file not matching after grompp

Hi, in general the error is self explanatory. It means that you have set more atoms in the topology file (usually that is the case). I would suggest a simple script in the language that you are most comfortable with, to count the occurrences of a specific element. Hope this helps.

[gmx-users] creating representative structures

Dear all, I have few questions regarding creating representative structures. For simplicity, let’s say I have a trajectory of 5 frames: 1. g_rmsf: After reading previous posts, here is what I understood. The average structures calculated using g_rmsf (by specifying –ox) is literally the