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

Dear Justin, Thank you very much for your reply. I inspected the thickness.xvg. There are number of columns in this file, I could not realize that which one is Z component of thickness. I also got averaged values using -oav option. How can I get the averaged values of Z component? Best

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

Dear Justin, Thank you very much for your reply. I have a confusion. There are 66 columns in thickness.xvg, and no header of the columns. How can I know the columns of z component? I think there are number of columns corresponding to x and y components. I averaged the all column, the values are

Re: [gmx-users] Simulation in vacuum

Dear Erik, Thank you very much for helping me. I have got 2 errors from grompp using gromacs v5.1. ERROR 1 [file nve.mdp]: With Verlet lists only full pbc or pbc=xy with walls is supported ERROR 2 [file nve.mdp]: With Verlet lists nstlist should be larger than 0 How can I fix these? I

Re: [gmx-users] Simulation in vacuum

Dear Erik, Thank you very much for your kind reply. Best regards, Mijiddorj > > -- > > Message: 3 > Date: Fri, 20 Jan 2017 19:01:10 +0900 > From: ? ? > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users]

[gmx-users] usage trjconv in membrane simulation

Dear gmx user, Hello, I complited calculation of KALP15 in DPPC. I would like to make further analysis such as generate structures of trajectory. I used following sequence of commands for gmx trjconv: 1. -pbc nojump 2. -pbc mol -ur compact 3. -pbc res (one case, ignored, but result is same) 4.

[gmx-users] gmx order has no output

Dear gmx users, I run heterogeneous membrane simulation which consists of several different type of lipids. Now I would like to analysis of order parameters. I used following command for sn-2 order parameters. gmx order -s ../step7_1.tpr -f ../nopbc.xtc -n sn2.ndx -od deuter_sn2.xvg -o

[gmx-users] Non-zero total charge and Floating Point Arithmetic

Dear gmx users, I got following note. Please advice me? I checked all topologies in my system, but I could not find floating point. NOTE 1 [file topol.top, line 36]: System has non-zero total charge: -14.97 Total charge should normally be an integer. See

Re: [gmx-users] Regarding topology...

> -- > > Message: 6 > Date: Tue, 14 Feb 2017 16:11:40 +0530 > From: Dilip H N > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Regarding topology... > Message-ID: >

[gmx-users] Simulation in vacuum

Dear gmx users, I would like to get experience of simulation in vacuum. Please suggest me tutorials, and advice me. I read about following comments which written on Shourjiya Sanyal tutorial. Can you discuss about it? In vacuum simulation, integration should be reduced compared to solvent phase

Re: [gmx-users] Per lipid area for heterogeneous membrane

Dear Justin, Thank you very much for your reply. I have a further question about GridMAT-MD tool. Is it possible to use in case with different upper leaflet and lower leaflet? In the manual, GridMAT-MD tool needs the leaflet tails face towards. Best regards, Mijee On 3/1/17 8:56 AM, ?

[gmx-users] Per lipid area for heterogeneous membrane

Dear gmx users, Hello, My simulation system consists of severil different type of membrane models including ergosterols. I want to analysis per lipid area for this system. How can I calculate the area? Please advice me. Can I use GridMAT-MD tool? If it is possible, how I do. Best regards, Mije

[gmx-users] terminated abnormally, message of GridMAT-MD tool

Dear Justin, I am using GridMAT-MD tool for analyses of heterogeneous membranes. I generated trajectory.gro only a group which contains a peptide and lipids. I got following Thread 1 terminated abnormally: Illegal division by zero at GridMAT-MD-parallel.pl line 501. What is the meaning of the

[gmx-users] temperature of simulated annealing

Dear gmx users, I would like to study folding properties of functional peptide using MD simulations both REMD and Simulated annealing. Can you give me advice following topic. How can I control the temperature of solution during the simulated annealing? For example, I am planning to increase

Re: [gmx-users] Replica exchange simulations more than number of processor

Dear gmx users, Thank you very much for your useful discussions. Best regards, Mijee On Sat, Apr 15, 2017 at 7:00 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To

[gmx-users] Replica exchange simulations more than number of processor

Dear gmx users, I would like to simulate folding of a peptides. I have only 12 core processor, and I assumed the number of replica using temperature generator as following link http://folding.bmc.uu.se/remd/. The number of replica is about 60. How can I solve this problem? Can you advice me,

[gmx-users] unusual GridMAT-MD tool result using gnuplot

Dear gmx users, I used the GridMAM-MD tool (v2) for the membrane thickness. After the gridmat-md, I used gnuplot for visualization. But there is no surface figure, there are bar code like lines. How can I fix these error? ​ thickness.bmp

Re: [gmx-users] Per lipid area for heterogeneous membrane

Dear Bjorn, Thank you very much for sending APL software information. I will ask you if there is a problem. Best regards, Mijee -- > > Message: 4 > Date: Thu, 2 Mar 2017 10:05:31 +0100 > From: Bj?rn Sommer > To:

Re: [gmx-users] Per lipid area for heterogeneous membrane

Dear Justin, Thank you very much. I analyzed 1001 frames of trajectory. All outputs are written in separate files. How can I summarize over all time? Best regards, Mijee > > On 3/2/17 12:34 AM, ? ? wrote: > > Dear Justin, > > > > Thank you very much for your reply. I have a further

[gmx-users] Fwd: unusual GridMAT-MD tool result using gnuplot

Thank you any advice. Best regards, Mijee -- Forwarded message -- From: Мижээ Батсайхан <b.mijidd...@gmail.com> Date: Tue, Mar 7, 2017 at 1:47 PM Subject: unusual GridMAT-MD tool result using gnuplot To: gromacs.org_gmx-users@maillist.sys.kth.se Dear gmx users,

[gmx-users] Most suitable intervals of temperature in REMD

Dear gmx users, Do you have a suggestions and discussions about most suitable temperature intervals for REMD simulations of the peptides? Best regards, Mijee -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] mdmat calculation of heavy atoms of two side chains

Dear gmx users, I would like to know about the hydrophobic interaction between heavy atoms of side chains in different chains of peptides. How can I use mdmat tool for this calculation? I separately indexed all heavy atoms but mdmat use only one index group in the calculation. I re-integrated

[gmx-users] use INTERFACE Force Field

Dear gmx users, I would like to use gromacs 5.1v with INTERFACE force field. Please, any advice and suggestions, thank you. Best regards, Miji -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] Hydroxyapatites parameter

Dear gmx users, I would like to simulate hydroxyapatites with biological molecules. How can I simulate this type of systems using groamcs? Are there any parameters for hydroxyapatite? Please. Best regards, -- Gromacs Users mailing list * Please search the archive at

[gmx-users] gmx mdmat calculation of heavy atoms of two side chains

Dear gmx users, I would like to know about the hydrophobic interaction between heavy atoms of side chains in different chains of peptides. How can I use mdmat tool for this calculation? I separately indexed all heavy atoms but mdmat use only one index group in the calculation. I re-integrated

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 1

Dear Justin, Thank you very much. Best regards, Mijee > > -- > > Message: 4 > Date: Mon, 31 Jul 2017 18:47:12 -0400 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] gmx mdmat calculation of heavy atoms of two >

[gmx-users] HSE in Charmm-gui membrane builder

Dear gmx users, I am sorry for asking about charmm-gui . I would like to use HSE protonation state of HIS, and I am using Charmm-gui membrane builder. But, Charmm-gui only produces HSD protonation state in my initial system. How can I use HSE state? Best regards, Mijee -- Gromacs Users mailing

[gmx-users] Non-bonded interaction energy

Dear gmx users, I would like to calculate non-bonded interaction energy between two groups. I performed mdrun -rerun for the groups. How reliable is sum of LJ and Coulombic energies? Please, is there any suggestion and discussion? Best regards, Mijee -- Gromacs Users mailing list * Please

[gmx-users] Atom OT1 in the residue

Dear gmx user, I am using gromacs 5.1 with charmm36-march2017 force field. I have an error as following: "Atom OT1 in residue DTRP 4 was not found in rtp entry DTRP with 24 atoms while sorting atoms." How can I fix this error? Additionally, I modified the structure of last DTRP residue from

Re: [gmx-users] Atom OT1 in the residue

Thank you for your answer. I modified the L-TRP structure to D-TRP structure, and the last version of charmm36 contains a topology of D-TRP. I used that one. Thanks. > > Dear gmx user, > > > > I am using gromacs 5.1 with charmm36-march2017 force field. I have an > error > > as following: > > >

[gmx-users] How to convert charmm str to itp file?

Dear Experts, I generated LIG.str file using CGenFF for a specific molecule. I would like to use GROMACS package. I tried to convert LIG.str file to LIG.itp file. I tried as following command using cgenff_charmm2gmx.py: ./cgenff_charmm2gmx.py LIG LIG.mol2 LIG.str charmm36 I got following error:

[gmx-users] regarding "-missing" option of pdb2gmx

Dear gmx users, I want to perform MD simulations of D-amino acid containing protein, and force field is charmm36, last version, which contains the parameters of D-amino acids. When I use pdb2gmx, I received following error: Fatal error: There were 10 missing atoms in molecule Protein, if you

Re: [gmx-users] regarding "-missing" option of pdb2gmx

Dear Mark, Thank you very much for your answer. In the modelled structure, there is no missing atoms. Actually, I used -ignh option for pdb2gmx, and it give this error. This error releated to the hydrogen atoms in the structure. It give me following warning: WARNING: atom HE3 is missing in

Re: [gmx-users] Atom OT1 in the residue

Dear Justin, Thank you very much your help. Best regards, Miji > -- > > Message: 2 > Date: Tue, 23 Jan 2018 06:44:59 -0500 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Atom OT1 in the residue > Message-ID: