Re: [gmx-users] Simulation of membrane protein

Justin, Could you tell me what difference in inflategro parameters ( cut-off for lipid removing and scaling factors) should I make for insertion protein in another bilayes in comparison tu tutorial ? Now I'm working with DMPC. I've inserted symmetrical alpha helices protein in this bilayer but in

Re: [gmx-users] Re: Problems with g_membed tools

I used the mdp file listed previously to generate the tpr file. It gave this warning: WARNING 1 [file membed.mdp]: Can not exclude the lattice Coulomb energy between energy groups then I ignored the warning with -maxwarn 1 and gave the tpr file to g_membed, command line like this: g_membe

[gmx-users] Charged wall

Hi Gmx Users, I am wondering whether is it possible in Gromacs to build sth like a charged wall to which the last residue of my terminal protein will be attached and run the simulation? I mean that the protein cannot move through some border which is attached to and which is positively or negative

[gmx-users] pull_distance

hi all. I need your advice. I have marked several atoms from one chain and several atoms from another chain (about 8 from each chain), they are forming 5 h-bonding places, and now I want to stabilize the distance between this chains during the MD. Can I use com pulling distance Y Y Y for it with

Re: [gmx-users] Insertion of the protein into membrane with Gmembed

James Starlight wrote: Dear Gromacs Users! I have some questions about insertion protein into membrane with Gmembed 1) I've used default parameters from gmembed manual for preparing input for insertion integrator = md energygrp = Protein freezegrps = Protein freezedim =

Re: [gmx-users] Re: mdp file problem

madhumita das wrote: Dear Justin, I could solve that perticular error but another problem has come, After running energy minimization, the sulphur and mercury(GG)atoms (present in the modified residue of cysteine named CYP at 182 position) break the bonds. Bonds don't break and form dur

Re: [gmx-users] Simulation of membrane protein

James Starlight wrote: Justin, Could you tell me what difference in inflategro parameters ( cut-off for lipid removing and scaling factors) should I make for insertion protein in another bilayes in comparison tu tutorial ? I've never made any changes; it's always worked just fine. Now I

Re: [gmx-users] pull_distance

Алексей Раевский wrote: hi all. I need your advice. I have marked several atoms from one chain and several atoms from another chain (about 8 from each chain), they are forming 5 h-bonding places, and now I want to stabilize the distance between this chains during the MD. Can I use com pull

Re: [gmx-users] Simulation of membrane protein

Thanks Justin I'll try to do that things. Some addition questions 1) About nvt and apt equilibration As I understood ref_t of the system must be equal to temperature of the phase transition of the specific LIPID. But in the npt and nvt.mdp files there are severl enties for ref_t ( for some sys

Re: [gmx-users] Simulation of membrane protein

James Starlight wrote: Thanks Justin I'll try to do that things. Some addition questions 1) About nvt and apt equilibration As I understood ref_t of the system must be equal to temperature of the phase transition of the specific LIPID. But in the npt and nvt.mdp files there are severl ent

Re: [gmx-users] Simulation of membrane protein

Justin, What temperature for NVT phase should be in gen_temp= 323 Does this parameere must be equal to the ref_t ? I've obtain strange results after NVT with ref_t = 297 297297 for protein in DMPC bilayer. The bilayer with water parts diffused in up and down direction of the box

Re: [gmx-users] orca question and LA

Dear Sir:   I want to know version of  groamcs and orca in your the qm/mm calculation? are they in parallel ? thank you!    --- 11年11月10日，周四, Micha Ben Achim Kunze 写道： 发件人: Micha Ben Achim Kunze 主题: Re: [gmx-users] orca question and LA 收件人: gmx-users@gromacs.org 日期: 2011年11月10日,周四,下午7:35

Re: [gmx-users] Simulation of membrane protein

James Starlight wrote: Justin, What temperature for NVT phase should be in gen_temp= 323 Does this parameere must be equal to the ref_t ? I've obtain strange results after NVT with ref_t = 297 297297 for protein in DMPC bilayer. You should generate velocities for the

[gmx-users] Charged wall

You could create an atomistic charged wall by placing atoms in a plane or grid and using position restraints or freeze groups to keep them in place. You could them use the pull code to restrain part of the protein relative to an atom(s) in this atomistic wall. You could obtain your desired

[gmx-users] GROMACS/ORCA QMMM

Dear GROMACS users, I'm trying to run a QM-MM optimization. I solvate my protein and add ions then I do a classical optimization (just GROMACS). After that I run grompp with the following minim.mdp file (just showing qmmm options): QMMM= yes QMMM-grps = Other QMmethod=

Re: [gmx-users] Simulation of membrane protein

Justin, It was a huge bilayer replacement on the magnitude comparable with the protein size. In more detailes both of the lipid leflets moved to the top and bottom side of the pb. The protein were placed on the old place ( due to the posres) so it turned out isolated from membrane :) Also I've f

Re: [gmx-users] Simulation of membrane protein

James Starlight wrote: Justin, It was a huge bilayer replacement on the magnitude comparable with the protein size. In more detailes both of the lipid leflets moved to the top and bottom side of the pb. The protein were placed on the old place ( due to the posres) so it turned out isolated

Re: [gmx-users] Simulation of membrane protein

Justin, 2011/11/11 Justin A. Lemkul > > > If the bilayer is splitting across periodic boundaries (I'm assuming > that's what you mean by "pb"), then it's more likely that you placed the > components of your system in an inconvenient way than it is that something > is actually wrong. > Bilayer

Re: [gmx-users] Simulation of membrane protein

James Starlight wrote: Justin, 2011/11/11 Justin A. Lemkul mailto:jalem...@vt.edu>> If the bilayer is splitting across periodic boundaries (I'm assuming that's what you mean by "pb"), then it's more likely that you placed the components of your system in an inconvenient way tha

Re: [gmx-users] Simulation of membrane protein

Justin, The system was compact after inserting protein into bilayer (I've obtain Area per lipid in accordanc with experimental reference) and futher minimization (only some llipid tails on the border of the system were distorded alittle) But after nvt simulation this discrepancy occured :) I've

Re: [gmx-users] Simulation of membrane protein

James Starlight wrote: Justin, The system was compact after inserting protein into bilayer (I've obtain Area per lipid in accordanc with experimental reference) and futher minimization (only some llipid tails on the border of the system were distorded alittle) But after nvt simulation thi

[gmx-users] g_wham and entropic subtraction

Hi,   I just wanted to check whether g_wham ( in gromacs4.5.4) already subtract the entropic contribution ( -2KTlog(r) term ) term when unbiasing the histogram obtained from umbrella sampling using distance in 3D as a reaction coordinate. Thanks Sanku-- gmx-users mailing listgmx-users@gromac

Re: [gmx-users] g_wham and entropic subtraction

On 2011-11-11 21:29, Sanku M wrote: Hi, I just wanted to check whether g_wham ( in gromacs4.5.4) already subtractthe entropic contribution ( -2KTlog(r) term ) term when unbiasing the histogram obtained from umbrella sampling using distance in 3D as a reaction coordinate. Thanks Sanku If it does

[gmx-users] UNK not found in residue topology

Hello, I'm getting an UNK not found in residue topology error message. I figured out what the error was and tried to add carbon to ffopslaa.rtf but it was unsucessful. What can I do/How can I change my pdb file from UNK so that Carbon and Hydrogen can be recognized? (I built my own hydrocarbon st

Re: [gmx-users] UNK not found in residue topology

Janowicz, Adrianna C. wrote: Hello, I'm getting an UNK not found in residue topology error message. I figured out what the error was and tried to add carbon to ffopslaa.rtf but it was unsucessful. What can I do/How can I change my pdb file from UNK so that Carbon and Hydrogen can be recognize

Re: [gmx-users] Positive potential energy for TFE solvent

On 11/11/2011 5:07 PM, Harpreet Basra wrote: Hi I am trying to generate an equilibrated box of 216 TFE molecules.To generate the 216 TFE molecule box i performed following steps: A suggested workflow can be found here http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation 1) I g

Re: [gmx-users] B-factor to large? Input for TLS

Hi Mark, Thanks for your reply. I will check if the reference structure and the trajectory fit. Cheers Henrey On Mon, Nov 7, 2011 at 9:15 PM, Mark Abraham wrote: > On 5/11/2011 11:05 AM, Henri Mone wrote: >> >> Dear Gromacs Users and Experts, >> >> I want to calculate from my xtc trajectory the

[gmx-users] Re: Using CHARMM 36 for DPPC simulation

Hi Everyone, I did another simulation where i found the the DPPC area per lipid is 0.61 nm^2 . Is this acceptable ? I have seen issues like this on the mailing list before can one of the experts give me some hints. Amit On Wed, Nov 9, 2011 at 12:24 PM, Amit Choubey wrote: > > 5Hello all, > >

Re: [gmx-users] Simulation of membrane protein

Justin, Indeed GenBox added insufficien of the SOL to my system due to the ussage of increased vdvdat ( I've used 0.350 value for the c atoms only but the were alot of void beetwen water and bilayer ) lipid_posres in Z directions have prevented the displacement of the bilayer but the water were

[gmx-users] picking out resident water molecule?

Hi everyone, I am doing MD simulation with a protein-ligand system, and I want to pick out the water molecules (their residue numbers or coordinates in any frame) that simultaneously contact (within 0.4 nm range for heavy atoms) the ligand and the protein, so that I could plot the lifetime of thes