[gmx-users] Simulating conjugated protein

Dear, gmx-users, Hello everyone, I'm simulating a peptide in an SDS micelle, where my peptide is conjugated to a organic compound at the N terminal. The SDS micelle was genrated using CHARMM-GUI, here I am stuck with a problem for adding atom types for the compound. I tried adding atomtypes for

[gmx-users] Calculating Eccentricity

Dear gmx user I am performing a MD simulation of peptides in sds for 100ns. After the completion of my production I am unable to remove the periodic boundary condition. I wanted to Calculate the eccentricity of the SDS micelle after 100ns, does the periodic boundary condition affect my

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 93

charset=windows-1252; format=flowed > > > > On 5/25/16 12:55 AM, Sanket Ghawali wrote: > > Dear, gmx-users, > > > > Hello everyone, > > > > I'm simulating a peptide in an SDS micelle, where my peptide is > conjugated > > to a organic compound

[gmx-users] Saving trajectory with different output time steps

Dear Gromacs user, I have 100ns trajectory in which the output steps are written every 5ps. I would like to save the same trajectory of 100ns with the output steps written at every 500ps. Is there any options available to do so ? Or do i need to perform the production run again making changes to

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 61

5/16/16 3:20 AM, Sanket Ghawali wrote: > Dear, gmx-users, > > Hello everyone, > I'm simulating a peptide in an SDS micelle. The simulation was > performed for 100ns > When I visualize the trajectory in VMD, the peptide moves to the SDS > interface where initially it was p

Re: [gmx-users] Calculating Distance

Thank you Justin. I am sorry, I didn't make my query specific. g_dist calculates distance between COMS of 2 groups with reference to time. I want to monitor the change in the COM of the peptide with respect to the initial position (COM) of the peptide at 0ns and not between COM of 2 different

[gmx-users] Production run error

*Dear all, I'm performing a production run for a 100ns simulation. It runs well upto 88 ns, but stops after that. Giving an error message.* Program mdrun_mpi, VERSION 4.6.5 Source code file: /root/data/gromacs-4.6.5/src/mdlib/domdec.c, line: 4412 Fatal error: A charge group moved too far between

[gmx-users] Calculating Distance

Dear, gmx-users, Hello everyone, I'm simulating a peptide in an SDS micelle. The simulation was performed for 100ns When I visualize the trajectory in VMD, the peptide moves to the SDS interface where initially it was placed in the center, the results are as expected. I would like to calculate

[gmx-users] Removing periodic boundary condition

Dear, gmx-users, Hello everyone, I'm simulating a peptide in an SDS micelle. The simulation was performed for 100ns When I view the trajectory in VMD, a portion of the SDS micelle moves to the right and goes into the next box. Of course, because of periodic boundary conditions. I tried using

[gmx-users] Preparing 30% TFE/Water simulation

Dear, gmx-users, Hello everyone, I wish to prepare a solvation box having 30% TFE/Water mixture. I would like too know how to calculate No of TFE and water molecules and what should be the ratio for No of TFE molecules / No of Water molecules. Any suggestions on how to go about doing this?

[gmx-users] DSSP

Dear all, How do i install DSSP for gromacs 5.1.1 I am curently working on Centos Which version should i download and any commands to install dssp Thanks & Regards Sanket -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] Binding Energy

Dear all Hello everyone, I'm simulating a peptide in an SDS micelle. The simulation was performed for 100ns I would like to calculate the binding energy between peptide and SDS over time. Thanks and Regards Sanket -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Varying results due to parallel processing (1 node versus 2 nodes)

Dear Gromacs users I am trying to simulate peptide in 30% TFE/water complex. Using parallel processing, I ran this system for 100ns using 2 nodes. The peptide is known to obtain helical conformation in this system. After 100ns, the peptide was found to be 37% helical. I ran the same system again

[gmx-users] Varying results due to parallel processing (1 node versus 2 nodes)

Dear Gromacs users I am trying to simulate peptide in 30% TFE/water complex. Using parallel processing, I ran this system for 100ns using 2 nodes. The peptide is known to obtain helical conformation in this system. After 100ns, the peptide was found to be 37% helical. I ran the same system again

[gmx-users] Cluster Analysis

Dear, gmx-users, I performed a cluster analysis using gmx cluster. I found a total of 178 clusters with the highest cluster having 63 members. I wish to save these members to a .trr or .pdb file in order to perform analysis on all these members as a whole and not on the representative structure

[gmx-users] Pore Size

Hi lists, I have performed a md simulation of peptides in sds micelle for 100ns. The peptides move to the interface after a time interval of 30 ns and remains there till 100ns. After visualizing it in VMD i see a pore formation in sds near the interface where the peptide is. I also see water

Re: [gmx-users] Pore Size

Thank you Pierre Ghesquiere i will surely try this out. -- Sanket B Ghawali Junior Research Fellow ICMR-Biomedical Informatics Centre National Institute for Research in Reproductive Health Parel, Mumbai. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Peptide orientation in lipid bilayers

Dear, gmx-user, Hello everyone, I am simulating a peptide in POPC:POPG lipid bilayer. Currently following the Tutorial 2: KALP15 in DPPC, I would like too know how to initially place the peptide 30 A away and parallel to one side of the lipid bilayer. Any suggestions on how to go about doing

[gmx-users] g(r)

Dear all Hello, Please let me know what is the unit of g(r) (nm or A) in the radial distribution function output(rdf.xvg) of the program g_rdf in gromacs. As the output shows no units. -- Sanket B Ghawali Junior Research Fellow ICMR-Biomedical Informatics Centre National Institute for Research

Re: [gmx-users] g(r)

sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. g(r) (Sanket Ghawali) >2. Re: g(r) (Mark Abraham) >3. Re: core dumped during