[gmx-users] How to calculate PMF after AFM pulling

Hello everybody, I have recently run a SMD with AFM method, and i got the .pdo file. But i don't know how to use the .pdo file to calculate the PMF profile. Could someone give me some suggestion? Thanks a lot. Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xu

Re: [gmx-users] Applying an improper to S-S bond

DimitryASuplatov wrote: Hello, The question is not actually about S-S. I have a covalent bond between Cys (SG atom) ang Tyr (CE atom) residues. I`ve corrected the specbonds.dat and oplsaa topology to create a new residue (tyr2) and I use cys2 topology for cystein. During the MD the this covalen

Re: [gmx-users] Using R.E.D. charges with OPLS AA

DimitryASuplatov wrote: Hello, I need to simulate a protein with deprotonated Tyr (HH hydrogen should be off). I used R.E.D. approach with PCGAMESS and RESP to calculate the charges. 1/ The problem is that to my understanding RESP charges apply to AMBER only. Am I correct? 2/ Can I use R.E.D

Re: [gmx-users] Usually how do you decide the salt concentration?

Peggy Yao wrote: Dear all, Usually how do you decide the salt concentration of the system? The salt concentration depends on a realistic physical model of whatever system you're examining. Note that in real biological systems, "salt" is a very broad, complex concept, so some approximatio

[gmx-users] Usually how do you decide the salt concentration?

Dear all, Usually how do you decide the salt concentration of the system? I got a protein structure from PDB, and what I am doing now is: to find out from which species the protein is extracted, and then search in google for the normal salt concentration of that species. However, it's hard to fin

[gmx-users] RE: Question for pulling in GROMACS 4.0

First of all it's best to post the error-message (i think there must be one). >From the pulling options below i would say the problem is probably that you >have 'pull_dim' and 'pull_geometry = direction', manual say 'pull_dim' is for >'distance' and 'position'. Another think is that you have in '

Re: [gmx-users] Applying an improper to S-S bond

DimitryASuplatov wrote: Hello, The question is not actually about S-S. I have a covalent bond between Cys (SG atom) ang Tyr (CE atom) residues. I`ve corrected the specbonds.dat and oplsaa topology to create a new residue (tyr2) and I use cys2 topology for cystein. During the MD the this coval

[gmx-users] Using R.E.D. charges with OPLS AA

Hello, I need to simulate a protein with deprotonated Tyr (HH hydrogen should be off). I used R.E.D. approach with PCGAMESS and RESP to calculate the charges. 1/ The problem is that to my understanding RESP charges apply to AMBER only. Am I correct? 2/ Can I use R.E.D. charges with OPLS AA? 3/

[gmx-users] Applying an improper to S-S bond

Hello, The question is not actually about S-S. I have a covalent bond between Cys (SG atom) ang Tyr (CE atom) residues. I`ve corrected the specbonds.dat and oplsaa topology to create a new residue (tyr2) and I use cys2 topology for cystein. During the MD the this covalent bond rotates a lot, so I

[gmx-users] Rosetta Academic Training Webinar

The Rosetta Design Group is proud to present the first webinar in the Rosetta Academic Workshop Series. For the first webinar, we have selected to focus on Protein-Protein Docking based on the answers to the interest poll. We hope this will be the first in a line of helpful and inspiring we

[gmx-users] Calculation of fraction of native contacts

Dear users, I just started using GROMACS and have trouble figuring out an efficient way to compute the fraction of native contacts for a trajectory. I've checked available options such as g_mdmat, g_dist, g_hbond and g_mindist as well as previous posts, but still are not able to make a side-by-sid

Re: [gmx-users] what factors effetc the simulation during energy minimization

bhargavi ch wrote: hi.. the sudden shoot up was observed in the RMS because of molecule breakage into monomer and dimer.we have also mutated some surface hydrophobic aminoacid and dint observe shoot up in any of the mutation. We have also observed the same shoot in the case of X ray crys

[gmx-users] factors effecting the simulation

hi.. We were working on the simulation of protein which has 3 chains (trimer) and each chain with a length of 80 amino acids. We have done the simulation for 5ns.We have observed a sudden shoot up in the RMS at 4ns so we continued simulating it to 10ns .The peak which started at 4ns extended till

[gmx-users] what factors effetc the simulation during energy minimization

hi.. the sudden shoot up was observed in the RMS because of molecule breakage into monomer and dimer.we have also mutated some surface hydrophobic aminoacid and dint observe shoot up in any of the mutation. We have also observed the same shoot in the case of X ray crystallographic structure of t

[gmx-users] (no subject)

hi.. I am working on the simulation of protein which has 3 chains (trimer)and each chain with a length of 80 amino acids. I have done the simulation for 5ns. I have observed a sudden shoot up in the RMS at 4ns so i continued simulating it to 10ns ..the peak which started at 4ns extended till 8ns

Re: [gmx-users] what factors effetc the simulation during energy minimization

bhargavi ch wrote: hi.. I have been doing the simulation of protein which has 3 chains (trimer)and each chain with a length of 80 amino acids. I have done the simulation for 5ns. I have observed a sudden peak at 4ns so i continued simulating it to 10ns ..the peak which started at 4ns extend

Re: [gmx-users] Explicit \ implicit

Bhawana Gupta wrote: Hello Everyone, I always use gromacs for doing explicit simulations. I want to ask whether i can do the implicit simulations by using gromacs. Whether there is any tutorial or manual from which i can understand it better. If not, Then Pls tell me how to do it implicitly.

Re: [gmx-users] Explicit \ implicit

Bhawana Gupta wrote: Hello Everyone, I always use gromacs for doing explicit simulations. I want to ask whether i can do the implicit simulations by using gromacs. Whether there is any tutorial or manual from which i can understand it better. If not, Then Pls tell me how to do it implicitly.

[gmx-users] Explicit \ implicit

Hello Everyone, I always use gromacs for doing explicit simulations. I want to ask whether i can do the implicit simulations by using gromacs. Whether there is any tutorial or manual from which i can understand it better. If not, Then Pls tell me how to do it implicitly. With Regards Bhawana

[gmx-users] what factors effetc the simulation during energy minimization

hi.. I have been doing the simulation of protein which has 3 chains (trimer)and each chain with a length of 80 amino acids. I have done the simulation for 5ns. I have observed a sudden peak at 4ns so i continued simulating it to 10ns ..the peak which started at 4ns extended till 8ns .i have extra

[gmx-users] pulling of molecule in GROMACS 4.03

Dear Sir, I want to pull a molecule called PRO from the lipid membrane DPP. To do this I have written the .mdp file as following from the help of gromacs mannual 4.0 . But when I try to make .tpr file from the .gro file, it says that "segmentation fault". Can you please wr

Re: [gmx-users] problem in simulation of DMPC lipid bilayer

Mark Abraham wrote: nitu sharma wrote: Dear all, I am using DMPC lipid bilayer from teleman sir website to insert my protein in this lipid bilayer .I have done this by using command genbox. After that when I have run the command - pdb2gmx -f tap-in-dmpc.pdb -o t

Re: [gmx-users] How to avoid the error:"Shake blockcrossing nodeboundaries"

Leontyev Igor wrote: I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulation 'pbc=no' which makes

Re: [gmx-users] How to make pdb file of whole trajectory

Bhawana Gupta wrote: Hello everyone, Thankyou for the reply for my previous message. But sorry to say I didn't get, what you want to say. Please tell me in elaborated way. I will be thankful. Your example commands look like you already have a trajectory file with the whole trajectory. Use t

Re: [gmx-users] How to avoid the error: "Shake blockcrossing nodeboundaries"

Igor Leontyev wrote: Leontyev Igor wrote: I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulat

[gmx-users] k means cluster

  Hi, Actually I was referring to the following post where the attempt to incorporate the method of k means clustering in gromacs has been discussed. http://www.mail-archive.com/gmx-users@gromacs.org/msg05089.html Has anyone tried to use this ? Thanks in advance Sarbani __

Re: [gmx-users] How to avoid the error: "Shake blockcrossing nodeboundaries"

Leontyev Igor wrote: I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulation 'pbc=no' which makes

Re: [gmx-users] How to make pdb file of whole trajectory

Bhawana Gupta wrote: Hello everyone, Thankyou for the reply for my previous message. But sorry to say I didn't get, what you want to say. Please tell me in elaborated way. I will be thankful. trjconv -sep With Regards Bhawana -

[gmx-users] How to make pdb file of whole trajectory

Hello everyone, Thankyou for the reply for my previous message. But sorry to say I didn't get, what you want to say. Please tell me in elaborated way. I will be thankful. With Regards Bhawana ___ gmx-users mailing listgmx-users@gromacs.org http://ww

Re: [gmx-users] How to avoid the error: "Shake block crossing nodeboundaries"

Igor Leontyev wrote: Leontyev Igor wrote: I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulation

Re:Re: [gmx-users] How to avoid the error: "Shake block crossing nodeboundaries"

Leontyev Igor wrote: I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulation 'pbc=no' which makes

Re: [gmx-users] problem in simulation of DMPC lipid bilayer

nitu sharma wrote: Dear all, I am using DMPC lipid bilayer from teleman sir website to insert my protein in this lipid bilayer .I have done this by using command genbox. After that when I have run the command - pdb2gmx -f tap-in-dmpc.pdb -o tap-in-dmpc.gro -p tap-i

Re: [gmx-users] k- means clustering

sarbani chattopadhyay wrote: Hi everyone, I want to know whether anyone has done k-means clustering using gromacs 3.3.1. I saw that one program has been contributed to do k-means clustering using "g_cluster". Has anyone tried to use this program to do such clustering. I

[gmx-users] k- means clustering

  Hi everyone, I want to know whether anyone has done k-means clustering using gromacs 3.3.1. I saw that one program has been contributed to do k-means clustering using "g_cluster". Has anyone tried to use this program to do such clustering. I would also like to know the

[gmx-users] problem in simulation of DMPC lipid bilayer

Dear all, I am using DMPC lipid bilayer from teleman sir website to insert my protein in this lipid bilayer .I have done this by using command genbox. After that when I have run the command - pdb2gmx -f tap-in-dmpc.pdb -o tap-in-dmpc.gro -p tap-in-dmpc.top -i tap-in-dmpc-it

Re: [gmx-users] How to avoid the error: "Shake block crossing node boundaries"

Leontyev Igor wrote: I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulation 'pbc=no' which make

[gmx-users] How to avoid the error: "Shake block crossing node boundaries"

I just switched from the version 3.3 to 4.0. It turned out that the 4.0 version does not allow to run a parallel simulation of my protein in vacuum. The protein consists of 2 chains and 4 separated (no bonds with chains) co-factors. For vacuum simulation 'pbc=no' which makes to use particle dec