[gmx-users] mdp file of membrane simulation

Dear users, I would like to simulate a system that consists of 3 different types of membrane models, peptides (they contain modified amino acid) and small molecule. In this case, I would like to know peptide-peptide, peptide-small molecule, peptide-lipid, and modified amino acid-small molecule int

[gmx-users] Mixed Solvents on gromacs v5

Dear users, Hello, I would like to simulate non-water/water solution system on gromacs v5. How can I use genbox -ci -nmol plugs on gromacs 5. Please advice me. Best regards, Mijiddorj -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GM

[gmx-users] Difference between POPI and DOPI membranes? and about lipid headgroups

Dear gmx users, I would like to simulate DOPI membrane system. I could not find DOPI membrane model from Charmm-gui, and I read that the closest one is POPI bilayer. I checked atoms of the lipids. First, there are carbons end of one tail needed to DOPI. Second, I need to change bond type from doub

Re: [gmx-users] Difference between POPI and DOPI membranes? and about lipid headgroups

Dear James, Thank you very much for your helpful suggestion. Best regards, Message: 3 Date: Wed, 19 Oct 2016 22:57:15 +0100 From: jkrie...@mrc-lmb.cam.ac.uk To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Difference between POPI and DOPI membranes? and about lipid headgroups Message

Re: [gmx-users] mdp file of membrane simulation

Thank you very much. *(1)* Which one is suitable the following 2 examples for energy groups in my mdp file? *Example 1* energygrps = Protein Membrane energy grps = r_1 Membrane energygrps = r_2 Membrane ... energygrps = r_N Membrane *Example 2* energygrps = Protein Membrane r_1 r_2 ... r_N *(

Re: [gmx-users] mdp file of membrane simulation

Dear Justin, Thank you very much. Best regards, Mijiddorj On 10/20/16 11:47 AM, Mijiddorj Batsaikhan wrote: > Thank you very much. > > *(1)* > Which one is suitable the following 2 examples for energy groups in my mdp > file? > > *Example 1* > > energygrps = Pro

[gmx-users] D-amino acids' force fields

Dear users, Hello, Is there any force field that contains parameters of D-amino acids? In my case I need to D-ILE and D-Phe amino acids simulation. Please, advice me. Best regards, Mijiddorj -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Li

[gmx-users] D-amino acids' force field

Dear users, Hello, Is there any force field that contains parameters of D-amino acids? In my case I need to D-ILE and D-Phe amino acids simulation. Please, advice me. Best regards, Mijiddorj -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Li

[gmx-users] renaming DILE to ILE for Charmm27?

Dear gmx users, I want to make a simulation the peptide that contains D-ILE using Charmm force field. Is it possible to rename the from DILE to ILE? and use pdb2gmx to generate topology of the peptide. Best regards, Mijiddorj -- Gromacs Users mailing list * Please search the archive at http:

[gmx-users] renaming DILE to ILE for Charmm27?

Dear gmx users, I want to make a simulation the peptide that contains D-ILE using Charmm27 force field. Is it possible to rename the from DILE to ILE? and use pdb2gmx to generate topology of the peptide. Best regards, Mijiddorj -- Gromacs Users mailing list * Please search the archive at htt

Re: [gmx-users] D-amino acids' force fields

alpha. For atomistic force fields you don't need to change anything, except the CMAP stuff in Charmm for the backbone dihedral, and you need to reset the hydrogen position if you used pdb2gmx for building the topology and the hydrogens. Cheers, Tsjerk On Oct 22, 2016 8:03 AM, "Mijiddorj Bat

[gmx-users] Two different force field use in one simulation?

Dear gmx users, I would like to simulate a system that consists of 2 different membranes and protein molecule. DOPI membrane model could not find from Charmm-gui ,embrane builder's models. I built the system DMPI membrane instead of DOPI. Then I modified DMPIs to DOPIs, and got charmm27 force fiel

Re: [gmx-users] Two different force field use in one simulation?

Dear Justin, Thank you very much. Can I use 2 different force fields in same simulation? It means charmm27 for the DOPI and charmm36 for other groups. Best regards, Mijiddorj > Dear gmx users, > > I would like to simulate a system that consists of 2 different membranes > and protein molecule

[gmx-users] LINCS warming, but continued EM

Dear gmx users, I manually added few atoms in my initial structure that was generated by Charmm-gui. Then I run EM, but early of minimization LINCS warns appeared, minimization continued and finished. (1) What can I do in this situation? (2) Is EM reasonable enough? Best regards, Mijiddorj --

Re: [gmx-users] LINCS warming, but continued EM

, Mijiddorj > > > On 10/28/16 12:35 PM, Mijiddorj Batsaikhan wrote: > > Dear gmx users, > > > > I manually added few atoms in my initial structure that was generated by > > Charmm-gui. Then I run EM, but early of minimization LINCS warns > appeared, > > minimizatio

[gmx-users] Bonds between P and O in bilayer head groups

Dear gmx users, I want to simulate membranes system using gromacs v5. Initial structure was built by Charmm-gui. Head groups' bonds between two O- and P are single in the Charmm topology file as a following: ATOM H11B HAL20.09 ! alpha4 ATOM PPL 1.50 !(-)

Re: [gmx-users] Bonds between P and O in bilayer head groups

Message-ID: <19c7bf46-e498-4c88-8828-c2bebe4f5...@vt.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > On 10/31/16 11:34 AM, Mijiddorj Batsaikhan wrote: > > Dear gmx users, > > > > I want to simulate membranes system using gromacs v5.

[gmx-users] Hydrophobic interaction analysis

Dear gmx users, I simulated several peptide's folding. I would like to know the effects of hydrophobic interaction for the folding. How can I make analysis and know the effect of hydrophobic interaction? Is it possible to assess the hydrophobic interaction using short range Van der Waals force?

[gmx-users] The Berendsen thermostat does not generate the correct kinetic energy distribution.

Dear gmx users, I want to simulation peptide on membrane. Initial structure was created by Charmm-gui, and Charmm-gui gave appropriate mdp files. I have a question about grompp's note. After energy minimization, I want to NVT equilibration, and grompp gave me one note as a following ** The

[gmx-users] Are the v-rescale thermostat and ld-seed suitable with md integrator?

Dear gmx_users, Hello, my simulation system consists of a protein and membranes using GROMACS. Initial structure was generated by Charmm-gui that gave the appropriate mdp files for the simulation. During the equilibration stage, Berendsen thermostat does not generate the correct kinetic energy dis

Re: [gmx-users] The Berendsen thermostat does not generate the correct kinetic energy distribution.

t; > http://dx.doi.org/10.1063/1.448118 > > > http://dx.doi.org/10.1063/1.2408420 > > > > > > And try to understand the differences between the two. Afterwards, you > > > should be able to make a choice suitable for your case. > > > > > > Best

Re: [gmx-users] Are the v-rescale thermostat and ld-seed suitable with md integrator?

ator? > Message-ID: <78b04a1b-c26d-ffed-ea21-35238530e...@vt.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > On 11/28/16 3:44 AM, Mijiddorj Batsaikhan wrote: > > Dear gmx_users, > > > > Hello, my simulation system consists of a pr

[gmx-users] COM group of Membrane and Protein simulation

Dear gmx_users, I started simulation that a peptide on membrane. My peptide locates on the membrane surface. I have two questions relating to the simulation. (1) When I start the simulation, I chose COM groups separately. Is this choice okay? or May I need to chose COM group inseparately? (2) Dur

Re: [gmx-users] COM group of Membrane and Protein simulation

ation > Message-ID: > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > On 12/1/16 9:17 PM, Mijiddorj Batsaikhan wrote: > > Dear gmx_users, > > > > I started simulation that a peptide on membrane. My peptide locates on > the > > me

Re: [gmx-users] COM group of Membrane and Protein simulation

ation > Message-ID: > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > On 12/1/16 9:17 PM, Mijiddorj Batsaikhan wrote: > > Dear gmx_users, > > > > I started simulation that a peptide on membrane. My peptide locates on > the > > membrane s

Re: [gmx-users] COM group of Membrane and Protein simulation

> Message-ID: > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > On 12/2/16 10:29 PM, Mijiddorj Batsaikhan wrote: > > Dear Justin, > > > > Thank you very much. > > I attached my mdp file. Peptide locates on membrane surface. I want to &

[gmx-users] Suitable techniques of self-assembly studies

Dear gmx users, Hello, I would like to investigate self assembly mechanism of fragment of the peptide using molecular dynamics simulation. I looked for the related techniques to the self assembly. I found several work using general molecular dynamics simulation. I think that simulated annealing me

[gmx-users] Inconsistent shifts

Dear gmx users, I simulated membrane and protein system. I would like to make analysis, and during the removing periodicity, I got the inconsistent shifts fatal error. How can fix this error? Can you help me? Best regards, Mijiddorj -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Inconsistent shifts

et=windows-1252; format=flowed > > > > On 12/14/16 2:06 AM, Mijiddorj Batsaikhan wrote: > > Dear gmx users, > > > > I simulated membrane and protein system. I would like to make analysis, > and > > during the removing periodicity, I got the inconsist

Re: [gmx-users] Inconsistent shifts

Dear Justin, Thank you very much. Best regards, Mijiddorj > > On 12/14/16 11:13 AM, Mijiddorj Batsaikhan wrote: > > Dear Justin, > > > > Thank you very much for reply. > > My commands > > > > gmx trjconv -s ../step7_1.tpr -f md.xtc -o md_nojump.xtc -pb

Re: [gmx-users] Homology model refinement

Hi, What is your target structure size? If you want to perform explicit solvent simulation for bigger protein, it may be time-consuming simulation. My suggestion is that you can run simulation implicitly, it helps you remove some bad contacts. Then, you can make cluster analysis and find dominatin

[gmx-users] LJ Interaction between 2 groups looks unusual

Dear gmx users, I run 500 ns simulation using GPU. After simulation I made mdrun -rerun. Finally, I performed gmx energy analysis. Result looks unusual as a following figure. LJ Interaction between 2 groups. ​ How is the figure? Is there any advice? Best regards, Mijiddorj -- Gromacs Users m

[gmx-users] How to choose z component of two groups

Dear gmx users, I am performing analysis of membrane system. I would like to estimate membrane thickness. I toke following command: gmx distance 0s topol.tpr -f traj.xtc -n selected_P.ndx -oav ave.xvg -oxyz thickness.xvg I do not know how to select z component of the two groups. Is there any

[gmx-users] Fatal error: Unknown bond_atomtype cn9 in Charmm27

Dear gmx users, I am using gromacs-v5.1 with charmm27 force field that extended by swissparams D amino acids. I got a following error. * Fatal error: Unknown bond_atomtype cn9 * I searched some solutions, but there is no cle

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 153, Issue 73

Dear Justin, Thank you very much for quick response. I want to capitalize cn9, but I could not find small cn9 in my force field. There is CN9 (capital) only for DNA. There is not any DNA molecules in my system. Best regards, Mijiddorj > > On 1/15/17 11:04 PM, Mijiddorj Batsaikhan

Re: [gmx-users] Fatal error: Unknown bond_atomtype cn9 in Charmm27

Dear Justin, Thank you very much for quick response. I want to capitalize cn9, but I could not find small cn9 in my force field. There is CN9 (capital) only for DNA. There is not any DNA molecules in my system. Best regards, Mijiddorj On 1/15/17 11:04 PM, Mijiddorj Batsaikhan wrote: > D

Re: [gmx-users] Fatal error: Unknown bond_atomtype cn9 in Charmm27

Dear Justin, Thank you very much. Best regards, Mijiddorj On 1/16/17 4:02 AM, Mijiddorj Batsaikhan wrote: > Dear Justin, > > Thank you very much for quick response. > > I want to capitalize cn9, but I could not find small cn9 in my force field. > There is CN9 (capital) o

[gmx-users] How can I calculate mutational free energy difference of wt and mutant protein?

Dear users, I want to make mutational free energy difference of a protein structure (delta G = G wild-type - G mutant). If you do not mind, please give me advice, and suggestions of related tutorials. Mijiddorj -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

[gmx-users] folding free energy difference of wt and mutant protein?

Dear users, I want to make mutational free energy difference of a protein structure (delta G = G wild-type - G mutant) in protein folding calculations. If you do not mind, please give me advice, and suggestions of related tutorials. Batsaikhan -- Gromacs Users mailing list * Please search the a

[gmx-users] Is simulated annealing mdp ok

Dear gmx users, I would like to explore two proteins interactions in water using simulated annealing. in my topology file, my proteins are named Protein and Protein2. I have following 2 hesitations: 1. How to set energy groups in mdp file? I wrote "define = Protein Non-Protein" 2. Is mdp f

[gmx-users] Is the any hydrophobic solutions?

Dear gmx users, I would like to simulate a structure of peptide in hydrophobic solution? Please give me advice and suggestions? Thank you. Best regards, Mijiddorj -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before po

[gmx-users] appropriate position restraint for stability of alpha helix

Dear users, Hello. I would like to simulate different length of alpha helices. I would like to find position restrain and other important parameters for stability of helix. What value of restrain appropriate for stable helix? Mijiddorj -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 18

I think that Husen, you shoud add your gromacs installed director /usr/local/gromacs/bin: to $PATH in /etc/bashrc. On Apr 5, 2016 6:00 PM, wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the Wo