[gmx-users] Umbrella sampling Tutorial by Dr. Lemkul

Hello, I was running the simulation for the umbrella sampling tutorial by Dr. Justin Lemkul in GROMACS 5.1.2 and I followed the steps exactly as they were mentioned. But in my summary_distances.dat there is one column. the COM column is missing. I am new to gromacs . So please help me out.

[gmx-users] Is charmm GUI ideal for membrane building

Hello everyone, I built a lipid membrane in Charmm-GUI and tried to equilibrate it in GROMACS 5.1.2. But the total energy goes on decreasing. Is it normal or should I try building the membrane by other methods. Thanks in advance, Amit Behera -- This message has been scanned for viruses and

Re: [gmx-users] Umbrella Sampling (Justin Lemkul)

Hello all, I was practicing the umbrella sampling tutorial by Dr. Justin Lemkul. In my summary_distances.dat file there is only one column ( the column for centre of mass is missing ). Can anyone say what possible mistakes I must have done. Regards, Amit Behera Dept. of Chemical Engg., IISc,

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 146, Issue 57

Hello, Thanks Tsjerk for the reply.So the equilibration needs to be run for some more time. Can I incorporate other force field in the membrane built from Charmm-GUI if the atom names are same in the forcefield as used by Charmm-GUI ? Regards, Amit Behera Dept. of Chemical Engg., IISc. > Date:

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 146, Issue 59

Hi Sotirios, What else should I check if I am trying to equilibrate a bilayer. Box size and temperature is okay. Any suggestions on what other quantity i should check ? Thanks, Amit Behera > Message: 1 > Date: Mon, 13 Jun 2016 07:29:51 + > From: "Sotirios Dionysios I. Papadatos"

[gmx-users] gmx rdf

Hello gmx_users, I was trying to plot distribution function in a bilayer system using gmx rdf. I used the system as a reference ( thinking it will take the COM of the system as reference point) . Then I plotted RDF of a marked atom. But it is plotting only in the positive direction while the

[gmx-users] gmx convert-tpr

Hello gmx_users, I was running a simulation and the wall time got exceeded in the cluster. I am thinking to use gmx convert-tpr. -extend (time) Does this method have any drawbacks. If so what other methods can I try to resume my simulation. Regards, Amit Behera Research Scholar Dept. of

[gmx-users] Tutorial #3 : Umbrella Sampling (By Justin Lemkul)

Hello, The summary_distances.dat file contains only one column ( the column for COM is missing). I am using GROMACS 5.1.2. How to solve this issue. Regards, Amit Behera Research Scholar, Dept. of Chemical Engineering, IISc -- Gromacs Users mailing list * Please search the archive at

[gmx-users] TRR file in VMD

Hello users, When I am loading data (.trr) into my structure file (.gro) in VMD. The trajectories are showing some kind of grid. It's like VMD is showing the path of a trajectory with actual lines. Can this problem be related to GROMACS-5.1.2 or do I need to change some settings in VMD ? Regards,

[gmx-users] Equilibration problem

Hello everyone, I prepared a bilayer using PACKMOL. Then ran energy minimisation. Till this point the structure completely intact. Then I ran nvt on the structure. At this point GROMACS-5.1.2 is giving back more than one pdb files (named step**.pdb) instead of usual .gro file. Does anyone know how

[gmx-users] electron density by gmx density

Hello Users, I was wandering how can we calculate the electron density with the help of gmx density. how to write the " -ei [<.dat>] (electrons.dat) " Regards, Amit Behera -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. --

[gmx-users] gmx distance

Hello users, I wanted to calculate Oxygen-Oxygen pair distance of a simple bulk water simulation. I made group of all the oxygen atoms using make_ndx. Now I am trying to use " gmx distance" : gmx distance -f water_whole.xtc -s water.tpr -n index.ndx -oav distances_oo.xvg But this is giving wrong

[gmx-users] GRID-MAT- area per lipid calculation

Hello Justin, I was trying to calculate area per lipid using GridMAT. But its giving back me the error : " Illegal division by zero at GridMAT-MD.pl line 761 " Can you help in finding the root of this error ? The bilayer just consists of one type of lipid and sol. Regards, Amit Behera --

[gmx-users] Regarding periodic boundary condition

Hello, After a run usually the molecules seems to be broken due to PBC . Do I need to convert this .gro file into another .gro file with whole molecule( using trjconv) before the next step. Will there be any difference in simulation results ? Regards, Amit Behera -- This message has been

[gmx-users] replacing lipid molecules with cholesterol

Hello, I built a system of lipid bilayer. Now I want to replace some of the lipid molecules by cholesterol molecules. Can anyone help me out in how to do that. Regards, Amit Behera -- Gromacs Users mailing list * Please search the archive at

[gmx-users] SETTLE constraint

Hello users, I was going through a literature ( dx.doi.org/10.1021/ct300342n ). Here they use GROMACS 4.5 version and use SETTLE constraint for bonds in water I wanted to know how can I apply SETTLE method in GROMACS 5.1.2. Regards, Amit Behera -- Gromacs Users mailing list * Please search the

[gmx-users] gmx wheel

Hello, I am trying to create a helical wheel. The format of .dat file is: No. of residues Names of the residues But it is giving error: Incorrect usage of option -f Can anyone help me with correct format ? Regards, Amit Behera -- This message has been scanned for viruses and dangerous

[gmx-users] Plumed with GROMACS 5.1.2

Hello, I have installed plumed 2.3. But I am having doubt in the patching process. Where should I patch the executable? Do I need to recompile gromacs after patching ? Thanks Amit Behera -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be

[gmx-users] GROMACS 4.6.4 vs GROMACS 5.1.2

Is there any major changes from version 4.* to 5.* that affects the stability of the a protein-lipid system ? I have been using GROMACS 5.1.2 but recently I got to know that GROMACS 5.1.* has some changes which affects long range LJ calculations which was not there in GROMACS 4.* . Can anyone help

[gmx-users] pdb2gmx

Hello users, I am using pdb2gmx on a protein. Fatal error: Residue 1 named LYS of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. ATOM 1

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 148, Issue 78

Hello Justin, I used gmx pdb2gmx -f protein.pdb -o protein.gro -ignh and I got the error: Program gmx pdb2gmx, VERSION 5.1.2 Source code file: /home/amit/Documents/gromacs-5.1.2/src/gromacs/gmxpreprocess/pgutil.c, line: 127 Fatal error: Residue 1 named LYS of a molecule in the input file was

Re: [gmx-users] pdb2gmx

Hi Justin, Here is the full screen output: Read 2236 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 285 residues with 2236 atoms chain #res #atoms 1 ' ' 285 2236 All occupancies are one Opening

[gmx-users] LINCS warning

Hello users, I was trying to energy minimize my system of protein embedded in bilayer. But I am receiving the following error: Step -1, time -0.001 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000942, max 0.149038 (between atoms 21616 and 21619) bonds that rotated more

[gmx-users] GROMACS-5.1.4 vs. GROMACS-5.1.2

Hello Everyone, I was initially using GROMACS-5.1.2. But in my institute cluster they have recently installed GROMACS-5.1.4. I just wanted to know will there be any difference in result between these two versions. Regards, Amit Behera -- This message has been scanned for viruses and dangerous

[gmx-users] gmx genrestr

Hello, I generated a distance matrix for C-alpha of the protein. I included in .top file too. But still when I am running grompp there is an error: NOTE 2 [file unknown]: disre = no, removed 45753 distance restraints Do I need to change anything else apart from justchanging the "define"

[gmx-users] keeping the pitch of helix constant

Hello, Is there any way in GROMACS-5.1.2 to keep the pitch of an alpha helix constrained. Regards, Amit -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] gmx do_dssp

Hello, Does the gmx do_dssp command works with dssp version 2.2.1 ? Regards, Amit -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Unstable Alpha Helix

Hello Justin, I am using "stride" program to analyze the helices. Can the Potential switch and other mdp parameters affect the stability of an Alphahelix. Regards, Amit > Date: Mon, 19 Dec 2016 08:06:29 -0500 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re:

[gmx-users] Unstable Alpha Helix

Hello everyone, I am trying to simulate an Alpha helix inside a bilayer. But a part of the alpha helix is loosing its form and converting into turns( while alphahelix should be stable in the bilayer environment) I am using Amber-99sb-ILDN for the protein and Slipids for the bilayer. I am using

Re: [gmx-users] QUERY IN GRO FILE

Hi, Yeah, both confout.gro and em.gro are same for the same tpr input file. The -deffnm flag is to indicate the names you want to give to your output files. Incase the -deffnm flag is missing GROMACS gives default names. Regards, Amit Behera REsearch Scholar, IISc, Bangalore. >

[gmx-users] mdrun error

Hello, After equilibrating my system for 100 ns( during which there was restraint on the protein letting the lipids to equilibrate), when I am trying to run my unrestrained run I am getting the following errors: 1. "bonds that rotated more than 30 degree" 2. "1 particles communicated to PME rank 0