[gmx-users] About gmx msd and membrane leaflets

Hello gromacs users: I want to obtain the lateral diffusion for a membrane with approximately 55 lipids+ions (NA+Cl) but i want to this for each leaflet of the membrane (outter and inner) and then obtain the average. I know that i can use gmx msd for lateral diffusion, but i don know how to k

[gmx-users] About membrane leaflets and msd

Hello gromacs users: I want to obtain the lateral diffusion for a membrane with approximately 55 lipids+ions (NA+Cl) but i want to this for each leaflet of the membrane (outter and inner) and then obtain the average. I know that i can use gmx msd for lateral diffusion, but i don know how to know

[gmx-users] Error No Such Moleculetype System

Hello Gromacs users: im running the following command gmx grompp -p file.top -c solvated.gro -f minimization.mdp -o minimization.tpr but the following error appear: No such Molecule type system (line 16). I know this is about the topology, but i don see nothing strane in line 16. Line 16 is syst

[gmx-users] About and index file of a monolayer...

Hello gromacs users: If i have a bilayer with lipids A & B and i want to create an index file for the upper and lower monolayer of one lipid, for example: lipid A-UPPER and lipid B-UPPER. Also, lipid A-LOWER and lipid B-UPPER. How can i do that using -n index.file? -- Gromacs Users mailing li

Re: [gmx-users] About rdf in membranes

: gmx-us...@gromacs.org Asunto: Re: [gmx-users] About rdf in membranes On 2/20/18 7:03 PM, Poncho Arvayo Zatarain wrote: > > Hello Gromacs Users: I want to calculate rdf in membranes. I read i need > something like .xy and i´m a little confussed. The command will be: gmx rdf > -f

[gmx-users] About rdf in membranes

Hello Gromacs Users: I want to calculate rdf in membranes. I read i need something like .xy and i´m a little confussed. The command will be: gmx rdf -f file.xtc -s file.tpr -n file.ndx -xy -o file.xvg= Thanks for your help -- Gromacs Users mailing list * Please search the archive at http://

Re: [gmx-users] Problems with trjconv

On 2/16/18 2:35 PM, Poncho Arvayo Zatarain wrote: > > Hello Gomacs users: I have a problem with a lipid bilayer. The bilayers is > inverted, the water is in the middle and the lipid tails are outside. How can > i flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s &

[gmx-users] Problems with trjconv

Hello Gomacs users: I have a problem with a lipid bilayer. The bilayers is inverted, the water is in the middle and the lipid tails are outside. How can i flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s file.tpr -n index -o file.gro -pbc whole but nothing happens. In index

[gmx-users] Flip a bilayer

Hello Gromacs users: I have a problem with a lipid bilayer, when i watch in vmd, is inverted, the water is in the middle and the lipid tails are outside. How can i flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s file.tpr -n index -o file.gro -pbc whole but nothing happens.

[gmx-users] Error in deuterium order parameters, index, nr

Hello gromacs users: i´m trying to graph my xvg of deuterium order parameters with the command: gmx order -s file.tpr -f fiile.xtc -n sn1.ndx -d z -od deuter_sn1.xvg but the following error appears: Error in user input: Invalid input lines in option nr. Required option was not provided and the

[gmx-users] Negative deuterium order parameters

Hello: I made 5 simulation: pure DPPC+a molecule inside, pure DPPE+molecule inside, 50% DPPC-50% DPPE+molecule inside, 75% DPPC-25%DPPE+molecule inside and 25%DPPC-75% DPPE+molecule inside. All the graphics were fine, but when i plot my system with 25%DPPC-755DPPE+Molecule inside the graphic o

[gmx-users] Making a move using command gromacs/vmd

Hello gromacs user: i want to make a movie using a gromacs command. I use this: gmx trjconv -s file.gro -f file.trr -pbc -o no jump -ndec 7 -o movie.gro. But it mrks me the following error: command line -o does not exist. So, i erase -o on "-o no jump" and marks me the error: invalid command:

[gmx-users] Plotting area per lipid

Hello gromacs users: I have the area per lipids for my dppc-dppe-protein membrane. But i want to plot the area per lipid vs time of simulation. When i use GridMAT it appears by residue. Can i still use this program to plot rea per lipid vs time of simulation? How that works? I all still with a

[gmx-users] Help: Illegal divion by zero lipid+protein+solvent

Hello gromacs users: I know this question is very common but i have this problem: I´m trying to obtain area per headgropu of a dppc+protein+solvent membrane and when i use GRIDMaAT it appears: illegal division by zero. My coord_file is my gro file, file type is gro, num_frames 1, num lipid t

[gmx-users] Illegal divion by zero lipid+protein+solvent

Hello gromacs users: I know this question is very common but i have this problem: I´m trying to obtain area per headgropu of a dppc+protein+solvent membrane and when i use GRIDMaAT it appears: illegal division by zero. My coord_file is my gro file, file type is gro, num_frames 1, num lipid type

[gmx-users] About msd and lateral diffussion command

Hello gromacs user: I want to obtain the msd and lateral diffussion for dppc/dppe membranes. I have this command: gmx msd -f file.tpr -s file.xtc -lateral z -rmcomm -beginfit 2 -endfit 13 -o msd.xvg <<< 2 3. Where 2 & 3 are dppc and dppe. Wht do you think about my command? It´s ok or i

[gmx-users] Calculate area per head group

Hello Gromacs users: I know there is not about Gromacs, but i want to calculate area per headgroup through simulation time. Anybody knos about a tutorial of GridMAT or can help me please? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Maili

[gmx-users] area per headgroup over the course of simulation

Hello gromacs user: i want to obtain the area per headgroup over the course of simulation of a dppc, dppe and dppc/dppe membranes. Does anybody know how to obtain it with a gromacs 5.0.2 command or with GridMat? i think is using GridMat, but how? Thanks -- Gromacs Users mailing list * Pleas

[gmx-users] Area per lipid through the time lipid membranes and mixed membranes

Hello gromacs user: I obtained the average area per lipid for dppc and dppe membrane, also for mixed membranes of dppc/dppe/embedded molecule. But i want to obtain the diagram of the area per lipid through the time, the course of my simulation for my dppc, dppe membranes and mixed membranes wi

[gmx-users] Makeing movies using VMD

Hello gromacs user: I want to do a movie of my simulation using vmd 1.9.1. I finished my simulation and i have my tpr, xtc file, etc. How can i do the movie using vmd and algo save it and attach it for paste it in a powerpoint? I only can watch the trajectory in vmd, vut not save it and put it

Re: [gmx-users] Error select a group gmx_density

: gromacs.org_gmx-users-boun...@maillist.sys.kth.se en nombre de Justin Lemkul Enviado: miércoles, 15 de febrero de 2017 08:02 a. m. Para: gmx-us...@gromacs.org Asunto: Re: [gmx-users] Error select a group gmx_density On 2/15/17 10:55 AM, Poncho Arvayo Zatarain wrote: > > Hello Gromacs users: I´m try

[gmx-users] Error select a group gmx_density

Hello Gromacs users: I´m trying to obtain the density og a mixed membrane plus a protein. I use the command line: gmx_gpu density -ng 4 -f npt.xtc -s npt.tpr -o density.xvg. And this appears: Reading file npt.tpr, VERSION 5.0.4 (single precision) Select 4 groups to calculate density for: Group

Re: [gmx-users] Trjconv problem invalid argument

Enviado: martes, 14 de febrero de 2017 09:53 a. m. Para: gmx-us...@gromacs.org Asunto: Re: [gmx-users] Trjconv problem invalid argument On 2/14/17 12:45 PM, Poncho Arvayo Zatarain wrote: > > > Hello Gromacs users: I want to obtain the density of a system using the > command: gmx_gpu

[gmx-users] Trjconv problem invalid argument

Hello Gromacs users: I want to obtain the density of a system using the command: gmx_gpu density -ng trjconv -f file.xtc -s file.tpr -o out.xtc -skip 100, but the following error appears: Invalid command argument: trjconv. What is wrong with trjconv? I am using gromacs 5.0.3 Thanks -- Gromac

[gmx-users] About gromacs density command

Hello gromacs user: i´m trying to obtain the membrane density of a dppc-dppe membrane, but i don´t know very well the command that i need to use. I have an idea: gmx_density -f file.xtc -n file.ndx -s file.tpr -ei file.dat -o file.xvg. File.dat corresponds to electrons.dat of dppc and/or dppe.

[gmx-users] Gro file does not match topology file... continue

Hello: according to the queshere abouttion and the answer send me here about gro (58674) file does not mtch with the topology (58666), i checked my gro file at the top corner on the left and said 58674, and at the end of the file the number of molecules is the same, 58674. i used TIP3 model an

[gmx-users] Gro file does not match topology

Hello gromacs users: I´m trying to do a minimization with 26 dppc 230 dppe 8960 water and 72 molecules of a compound. But when i used grompp the following error appears: gro file (58674) does not match with top file (58666). Also i tried with 8961 molecules of solvent and the same error appears

[gmx-users] Atomtype CG311 not found

Hello everyone: i´m trying to minimize a dppc-dppe-heta membrane, using charmm36. But when i use the grompp i have the following error: line: 1353 Fatal error: Atomtype CG311 not found. My topology includes: include "toppar/charmm36.itp" include "toppar/DPPE.itp" include "toppar/DPPC.itp" includ

[gmx-users] About negative values deuterium order parameters

Some days ago i send a quetion about negative values of deuterium order parameters in a 25% DPPC 75% DPPE+ nesthesic membrane. Thomas Piggot repond to me about the Scd que be negative too, specially for DPPC and DPPE. Now i send my obatained values for Scd. It is correct to have negative value

[gmx-users] Order parameters negative value

Hello: I´m analyzing the order parameters of a mixed membrane (25% dppc-75% dppe), but some of the values are negative and the graphic is not like the commons. Is this fine? the values for order parameters can be negative? what means negative values in an order parameters? -- Gromacs Users ma

[gmx-users] grp 1 does not have same number of elements as grp 1

Hello: I want to analyze order parameters for a 128 molecules of DPPC/ 128 moleculesDPPE/Drug membrane, but when i run gmx_order -s npt.tpr -f npt.xtc -n sn1.ndx -d z -od deuter_sn1.xvg, the following error appears: grp 1 does not have same number of elements as grp 1. I deleted 0-3 (System

[gmx-users] grp 1 does not have same number of elements as grp 1

Hello: I want to analyze order parameters for a 128 molecules of DPPC/ 128 moleculesDPPE/Drug membrane, but when i run gmx_order -s npt.tpr -f npt.xtc -n sn1.ndx -d z -od deuter_sn1.xvg, the following error appears: grp 1 does not have same number of elements as grp 1. I deleted 0-3 (System, DPP

[gmx-users] About atom references calculating area per lipid

hello: i´m trying to calculate area per lipid of mixed bilayer using Gid-MAT for a membrane of 128 DPPC and 128 DPPE and a mixed 128 DPPC+128 DPPE+Drug. My atom reference for DPPC is P, so ¿the atom reference for the DPPE need to be necesarili the P too?. Because when i run this, the result va

[gmx-users] About Area per lipid using Gid-MAT Continuation...

Hello Justin: Following with the error on my Grid-MAT-MD.pl line 761. This is my param_exampe using in Grid-MAT for calculate area per lipid in DPPC/DPPE bilayer Input file and input file parameters coord_file: dppc128+dppe128+hlt+tip3.gro file_type: gro num_frames:1 n

[gmx-users] About Area per lipid using Gid-MAT

Hello: I'm calculating the area per lipid of a mixed bilayer of dppc and dppe with a molecule inside, using GRID MAT. When i run Grid Mat it appears: Can't calculate the are per lipid, line 761 can't divided by zero in GRID-MAT-MD.pl. So, i check de Grid-MAT.pl in line 761 and this is in: Whic

[gmx-users] About Area per lipids in Mixed Membranes

Hello: I want to calculate the area per lipids in DPPC/DPPE membranes of 128 lipids per leafleft. I have a membrane with 128 DPPC and 128 molecules ofDPPE and Box X and Box Y are 8.846591 and 8.846591 respectivelly. Should i calculate the area per lipid using (Box X * Box Y)/(#lipids per leafl

[gmx-users] RV: About Deuterium order parameters

Hello gromacs users: I want to determine the deuterium order paramters for a dppc using gromacs 5.0.4 and i use the command: make_ndx -f npt.tpr -o sn1.ndx. Also i know that i need to do it too for sn2.ndx. But my question is: Should i make the index this way: > a C34 > a C36 > a C37 > a C38 .

[gmx-users] About Deuterium order parameters

Hello gromacs user: I want to determine the deuterium order paramters for a dppc using gromacs 5.0.4 and i use the command: make_ndx -f npt.tpr -o sn1.ndx. Also i know that i need to do it too for sn2.ndx. But my question is: Should i make the index this way: > a C34 > a C36 > a C37 > a C38

[gmx-users] Command line extend npt

Hello: This is my command lines when i want to extend to 50 ns: I´m using gpus gmx_gpu tpbconv -s npt.tpr -extend 5 npt02.tpr gmx_gpu mdrun -v -deffnm npt02 -cpi npt.cpt And the program (Gromacs 5.0.2) says: Can not open file: npt02.tpr Also, in my carpet i only have the npt.tpr, not npt

Re: [gmx-users] About extend npt

-users] About extend npt Hi, We need to see your actual copied and pasted command lines and error messages before we can give feedback on what might be wrong. Mark On Wed, 14 Sep 2016 18:09 Poncho Arvayo Zatarain wrote: > > > Hello. I did a 10 NPT but i want to extend to 50 ns and i´m

[gmx-users] About extend npt

Hello. I did a 10 NPT but i want to extend to 50 ns and i´m using the command gmx_gpu tpbconv file.tpr -extend 5 file02.tpr and mdrun -v deffnm file02 -cpi npt.cpi. In my folder i only have the npt.tpr that i think i should use as "tpr.file" but, what about file02.tpr and file02, should i

[gmx-users] You are applying a switch function to vdw forces or potentials from 0 to 1.2 nm

Hello: i'm running the grompp of NVT but during the run i have the following:NOTE: You are applying a switch function to vdw forces or potentials from 0 to 1.2 nm, which is more than half the interaction ranges whereas switch functions are intended to act only close to the cut-offWhat does it m

[gmx-users] The bond in molecular type DPPC between atoms 31 C21 y 32 022 has an estimated oscillational period of 2.1e-02 ps, which is less than 5 times the time step of 1.0e-01 ps

Hello. I' ḿ simulating a DPPC membrane with TIP3 water model and charmm36 forcefield and in the grompp of NVT equilibration i have this warning: (Warning 1: file topol.top line 24) The bond in molecular type DPPC between atoms 31 C21 y 32 022 has an estimated oscillational period of 2.1e-02 ps,

[gmx-users] About The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element

Hello, due to one of my last question and about the error: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. How can do large the box? My .gro files vectors are 8.9 8.90 and 7.90

[gmx-users] The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element

Hello, i ḿ working in a lipid bilayer using charmm36 forcefield and trying to do NVT equilibration but when i use grompp for nvt i receive the folowing error: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size o

[gmx-users] Segmentation fault (core dumped) after grompp minimization

Hello, i'm working with a 256 phospholipid membrane and i run grompp for minimization and to generate a .tpr file, so after run grompp i run the mdrun but instantly crushed with the legend: SSteepest Descents: Tolerance Fmax: 1.e03. No. of steps: 50,000, nan Fmax: inf, atom: 30983. Segmentat

[gmx-users] Tau-t should be at least 20 times larger than nsttcouple*dt

Hello users: I want to run a simulation with MD run of DPPC+DPPE+Ligand+Water using the command gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_1.tpr but when i used it the following warning and error appears:Warning: For proper integration of the Nose-Hoover thermo

[gmx-users] Nvt T-coupling error

I`m running a simulation of dppe+dppe+ligand+wáter and i`m building index with the command gmc make_ndx –f minimiz-gro –o index.ndx. When i use the command the following options appears to build the index: 0 System27592 atoms 1 Other 27592 atoms 2 LIG

[gmx-users] DPPC hlothane Residue DPP not found in residue topology database

Hello: Concerning about my last question of DPPC membrane and halothane simulation and the GROMOS 53a6. When i used pdb2gmx the following error appears: Residue DPP not found in residue topology database. Then, i googled to Gromacs webpage and i found XXX'_not_found_in_residue_topology_database

[gmx-users] Protein-ligand error pdb2gmx

Hello: I made the Apoferritin-T4 Lysozyme tutorial of Justin, then i change the ligand and simulated Apoferritin with an anaesthesic (halothane) and everything is fine. I tried to run a third simulation using halothane as ligand and DPPC instead of Apoferritin. I have a folder of gromos53a6.ff

[gmx-users] Halothane rtp and pdb file

Hello, i want to run a simulation of halothane in a DPPC membrane. I have the pdb file of halothane and run the pdb2gmx (pdb2gmx -f halotano.pdb -o halotano.gro -water spc) with GROMOS 53a6 forcefield and the rtp file. The output marks this: Warning starting residue i825, 1493, -1442, -01715,

[gmx-users] Fatal error pdb

Hello: I'm trying to simulate an halothane molecule in water. I download the halothane at pubchem and converted to pdb format using open babel 2.3.2 but when i use pdb2gmx and select OPLS/AA forcefield it appears: Fatal e

[gmx-users] No such moleculetype DPPE

Hello: i'm working in a simulation for a DPPC/DPPE membrane and when i use the instruction grompp -f minim.mdp -c dppc-dppe128.pdb -p topol_dppc.top -o em.tp for enrgy minimization, the following error appears: Fatal error: No such moleculetype DPPE, so it appears some warnings like: File ffnon

[gmx-users] DPPC/DPPE minim.mdp

Hello, i want to simulate a 128 DPPC molecule, 3655 water molecules but with 25% of DPPE. I replace de 25% of 128 DPPC molecules with DPPE and i'ḿ using the same forcefield and topology reported by Lemkul in his KALP15 in DPPC tutorial. When i want to minimize the energy i use the command line

[gmx-users] gmx distance

Helecho "3 4"| g_distlo, i want to introduce a coomand in Gromacs 5.0.4 with the initial echo "3 4"| g_dist. Should i use gmx distance echo "3 4"| g_dist and the rest of the commnand? This is the complete command i want to use echo "3 4"| g_dist -f dppc128_1-nj-ct-nobox.xtc -s dppc128_1.tpr -o

[gmx-users] g_dist tools

Hello, i want to run this command: echo "3 4"| g_dist -f dppc128_1-nj-ct-nobox.xtc - s dppc128_1.tpr -o dppc128-Dpp.xvg -n Dpp.ndx -b 2 in Gromacs 5.0.4 but when i run it, the following appears: This tool has been removed. Please see tool changes for 5.0. And when i see th tools appears: g_

[gmx-users] Invalid command line argument

Hello: I'm doing Martínez Seara simulation and i want to run this command: echo "0"|trjconv -f dppc128_1-nj-ct.xtc -s dppc128_1.tpr -o dppc128_1-nj -ct -nobox.xtc -box 100 100 100 but it appears: Invalid command line argument: -nobox.xtc Iḿ using GROMACS 5.0.2 and working in a cluster. What can

[gmx-users] gromos53a6_lipid.ff/forcefield.itp not found

From: poncho_8...@hotmail.com To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: gromos53a6_lipid.ff/forcefield.itp not found Date: Wed, 27 May 2015 14:50:27 -0300 Hello i'm doing a simulation and when i use grompp grompp -f dppc128.mdp -c dppc128_40ns.pdb -p dppc128.top -o dppc128_1.tpr

[gmx-users] gromos53a6_lipid.ff/forcefield.itp not found

Hello i'm doing a simulation and when i use grompp grompp -f dppc128.mdp -c dppc128_40ns.pdb -p dppc128.top -o dppc128_1.tpr i have this: Fatal error: Topology include file "gromos53a6_lipid.ff/forcefield.itp" not found. What should i include in my topolofy files? And i have 2 notes: NOTE 1 [fil

[gmx-users] trjconv command not found

Hello, when i use the command echo "0"|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 i have this: command not found: trjconv. What can i do? Alfonso -- Gromacs Users mailing list * Please search the archive at http://www.gro

[gmx-users] Re generate a tpr file

i'm trying to use the following command echo "0"|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 but it appears the following error reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I'm doing Martinez Seara tutorial and in the article uses 4.0.2 gromac

[gmx-users] Fatal error tpx file

I' m running Martínez Seara dppc tutorial and when i use echo "0"|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it

[gmx-users] Version 100 with version 83 program

I' m running Martínez Seara dppc tutorial and when i use echo "0"|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it has

[gmx-users] Version 100 with version 83 program

I' m running Martínez Seara dppc tutorial and when i use echo "0"|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it has to be

[gmx-users] Version 100 with version 83 program

I' m running Martínez Seara dppc tutorial and when i use echo "0"|trjconv -f dppc128_1.xtc -s dppc128_1.tpr -o dppc128_1-ini.gro -dump 10 it appears the following error: Fatal error: reading tpx file (dppc128_1.tpr) version 100 with version 83 program. I' m using Gromacs 4.6.5 maybe it has to be

[gmx-users] .gro error

Hello, i'm working on membrane thickness in Martínez-Seara dppc article. When i use the following command: printf "%s\n" "r 1-64 & a P" "r 65-128 & a P" "q"|make_ndx -f dppc128_1.gro -o Dpp.ndx The following error appears: File Input/output error: dppc128_1.gro. Could you help me to solve it pl

[gmx-users] Syntax error -File dppc.itp line 1

Hello, im doing a DPPC simulation and when i use grompp to generate tpr file this appears: Fatal error: Syntax error -File dppc.itp, line 1. Last line read: '[moleculetype]' Invalid order for directive moleculetype. What can i do? My dppc.itp includes [ moleculetype ] ; Name nrexcl DPP

[gmx-users] File input/output error: algorithm_parameters.mdp

Hello, i´m working in a tutorial to generate a tpr file and i´m using grompp, my mdp file, .pdb and .top file, -o and .tpr file. I´m using this command for grompp: grompp -f dppc128.mdp -c dppc.pdb -p topol_dppc.top -o dppc128_1.tpr And it appears two errors: File input/output error: algorithm_

[gmx-users] FW: Sending an email, question

> Hello, i I´m trying to replicate a DPPC128 membrane simulation of the Article > Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do > It of Martínez-Seara et al. This is mi mpd file and i´m using GROMACS 5.0.2 > Title: MD SIMULATIONintegrator : md dt : 0.002 nsteps :

[gmx-users] Sending an email, question

Hello, i´m new here and i have a question. I´m trying to replicate a DPPC128 membrane simulation of the Article Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do It of Martínez-Seara et al. This is mi mpd file and i´m using GROMACS 5.0.2 Title: MD SIMULATIONintegrat