Re: [gmx-users] MD of two structure together-receptor+ligand

Nikhil Follow Justin's tutorial for protein-ligand MD. You might want to view Hbonds between inhibitor and protein, for that Hbond mapping helps. You can also calculate binding energy. If the protein has specific conformation, you can view the frames for any structural change or stability.

[gmx-users] Non standard or modified amino acids

Hello all I am doing a protein peptide MD. Can anyone suggest how to obatin topology file for modified peptides or non-standard amino acids? Best Wishes Suniba Sent from my iPhone -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Non-Integral Charges

Hello Everyone I want to know how to change the non-integral charges? I am simulating a pentameric model of protein in water and the net charge comes out to be -5.0. Everything goes ok till final mdrun. As soon as its started, it carshes. Is it dus to wring topology as the charges are

Re: [gmx-users] Simulating a protein dimer

I encountered similar problem after simulating a pentameric model of protein. It was solved by applying pbc whole in gmx trjconv. Sent from my iPhone > On 07-Jun-2016, at 7:49 pm, Biplab Ghosh wrote: > > Dear Gromacs Users, > > I am trying to simulate a protein dimer

Re: [gmx-users] allosteric effect

Hi Qasim You can read below mentioned paper for analysis: http://www.nature.com/articles/srep23830 Sent from my iPhone > On 03-Jun-2016, at 3:28 pm, Qasim Pars wrote: > > Hi Tsjerk, > > I am interested in the dynamic and conformational effect of allostery on > protein.

Re: [gmx-users] Extending the MD

..@gmail.com> wrote: >> >> It may be a case. You can rename the files to what they were and try >> again. Since here, the error simply implies the files are renamed or >> missing. >> >> Sapna Mayuri Borah >> c/o Dr. A. N. Jha >> Research

Re: [gmx-users] Extending the MD

file of the > simulation run, that will be state.cpt in your case.. Hope you have > mentioned that. Ignore if you have :) > > Sapna Mayuri Borah > c/o Dr. A. N. Jha > Research student > Tezpur University, > India > >> On Thu, May 26, 2016 at 4:38 PM, sun <sun

[gmx-users] Extending the MD

Hello I started a 100 ns ns pro-lig simulation which was terminated accidently at 53.33 ns. Then I restarted simulation with checkpoint file and simulation ended at 100 ns. Now I have the md_0_1.tpr and next.tpr files which were generated for 53.33 and 100 ns data reapectively and log, trr

Re: [gmx-users] Extending the MD

rting the tpr, while initiating mdrun, try adding the previous > cpt file as well.. > > mdrun -s next.tpr -cpi previous.cpt > > Thanks! > > > Sapna Mayuri Borah > c/o Dr. A. N. Jha > Research student > Tezpur University, > India > >> On Thu, May 26

[gmx-users] Block averaging

Hello users and experts I have completed a 200 ns protein ligand simulation using GROMOS 43a1 and Gromacs v 5.0. I expected to observe a conformational change in protein in the presence of ligand and the results are as expected and correlates to previous references as well. So, shall i believe

Re: [gmx-users] Block averaging

Allright Sir Thank you Sent from my iPhone > On 22-Jun-2016, at 7:09 pm, Justin Lemkul <jalem...@vt.edu> wrote: > > > >> On 6/22/16 5:02 AM, sun wrote: >> Hello users and experts I have completed a 200 ns protein ligand simulation >> using GROMOS 43a1 and

[gmx-users] PCA

Hello Users and Experts Can anyone please suggest me good papers in which authors have performed principal component analysis and then projected the free energy landscape onto first two eigen vectors. I am confused as different studies give different results and used different parameters for

Re: [gmx-users] Block averaging

. Sent from my iPhone > On 22-Jun-2016, at 7:09 pm, Justin Lemkul <jalem...@vt.edu> wrote: > > > >> On 6/22/16 5:02 AM, sun wrote: >> Hello users and experts I have completed a 200 ns protein ligand simulation >> using GROMOS 43a1 and Gromacs v 5.0. I

Re: [gmx-users] Water removed from system and visualizing protein alone in VMD. But problem in visualization of all frames

Problem solved! Thank You very much. Sent from my iPhone > On 05-Feb-2016, at 3:20 pm, Mark Abraham wrote: > > Hi, > > That works, but only if your full trajectory is small enough to fit in > memory! > > Mark > >> On Fri, 5 Feb 2016 09:05 Nikhil Maroli

Re: [gmx-users] Water removed from system and visualizing protein alone in VMD. But problem in visualization of all frames

If I change the representation then the problem occurs actually. Its fine with trajectory, for 10ns, 1001 frames are loaded in VMD. But when I play to visualize, the protein does not move at all. I mean, only one conformation remains in all frames which is not possible, I believe. This error

[gmx-users] Water removed from system and visualizing protein alone in VMD. But problem in visualization of all frames

Hello Everyone I have performed a md simulation if protein in water for 10ns and frames were obtained after every 10ps. I wanted to visualize the.gro and trajectory file in VMD, without water, so I prepared an index file containing protein only. Using editcon i removed water from md.gro as well

Re: [gmx-users] Temperature or Pressure Coupling

016, at 4:49 pm, "VITALY V. CHABAN" <vvcha...@gmail.com> wrote: > > yes > > > >> On Tue, Jan 26, 2016 at 3:42 AM, sun <sun.i...@gmail.com> wrote: >> >> Hello >> I want to simulate a protein in water and observe its behavior alone and &

[gmx-users] Temperature or Pressure Coupling

Hello I want to simulate a protein in water and observe its behavior alone and then in the presence of ligand. I have read somewhere that NPT MD is best for pro-lig complexes as it resembles the in vitro and in vivo conditions (conformational changes,biomolecular reactions, binding etc.). So

[gmx-users] Modified peptides

Hello I want to do protein-ligand MD with Gromos-43A1 ff. My ligand is a tripeptide with a heterocyclic ring attached to -N terminus. I read in Justin's tutorial, for non-peptidic ligands, one can obtain co-ordinates from PRODRG server. My question is, if i can obtain the co-ordinates for

[gmx-users] gmx cluster

Hi Everyone I performed a 10ns MD using Gromos 43a1 ff and obtained frames at 10ps interval. However, When i gave gmx cluster command, I obatined 661 clusters. Does this indicate my proteini is not stable? However When i viewed trajectory in VMD, it seems good with least fluctuations in

Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

What marks means clearly- you should use second equilibrium output file for final mdrun. i.e. posre_nvt Sent from my iPhone > On 31-Mar-2016, at 12:17 am, Mark Abraham wrote: > > Hi, > > The reasoning behind doing equilibration is covered in various tutorials, >

[gmx-users] Extending the simulation

Dear Gromacs Usre I have performed a 10 ns MD simulation with Gromos 43A1 ff. Now I want to extend the simulation from 10 ns up to 100 ns. Would anyone tell me the most appropriate of continuing simulation? Thank You With Regards Suniba Sent from my iPhone -- Gromacs Users mailing list *

Re: [gmx-users] Extending the simulation

Yes I have done it now. Thank you so much guys.  Sent from my iPhone > On 07-Mar-2016, at 4:32 pm, jkrie...@mrc-lmb.cam.ac.uk wrote: > > This page is now a little out of date. GROMACS 5 has replaced tbpconv with > gmx convert-tpr but otherwise the instructions are the same. > >>

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

I think using -ignh does not "remove" hydrogens. Hence, you can use it. Sent from my iPhone > On 30-Mar-2016, at 6:04 pm, rajendra kumar wrote: > > Hi, > > As suggested above, use -ignh to ignore hydrogen atoms. To use a specific > Histidine, you may change residue name HIS

[gmx-users] Modified peptides

Hello Gromacs Users I have already posted this query but in the absence of any suggestion, I am posting it again. I hope someone will help me. I am going to do protein-peptide MD using Justin's protein-ligand tutorial (ff gromos43A1, GROMACS version 5.0). My ligand is a pentameric modified

Re: [gmx-users] autocorellation function

What kind of errors and please explain your system. Sent from my iPhone > On 04-Apr-2016, at 5:45 am, "novice...@hotmail.com" > wrote: > > Hi all, > > > I want to calculate the autocorrelation function of the system. I typed gmx > analyze -ac. but I keep getting

Re: [gmx-users] autocorellation function

application called MPI_Abort(MPI_COMM_WORLD, 1) - > process 0 > [2016-04-04T04:41:34Z]: Exited with code 0 > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of sun

Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

I have not looked at your link yet but I believe PyMol is best for generating high quality figures. You can explore a number of options in pymol. Regards Suniba Sent from my iPhone > On 30-Mar-2016, at 3:15 am, bio hpc wrote: > > Hi, > > after a protein-ligand

Re: [gmx-users] uninstall gromacs 5.0

sudo apt-get uninstall Gromacs-5.0 Sent from my iPhone > On 23-May-2016, at 6:51 pm, Anurag Dobhal > wrote: > > Dear Users: > > I want to uninstall gromacs 5.0 and replace it with gromacs 5.1. > The link provided in the gromacs website (Removing a

Re: [gmx-users] uninstall gromacs 5.0

I am so sorry Mark It sudo apt-get remove Gromacs :) I used this in Ubuntu. Also, for Gromacs and its dependencies: sudo apt-get remove --auto-remove gromacs I hope this works Sent from my iPhone > On 23-May-2016, at 9:49 pm, Mark Abraham <mark.j.abra...@gmail.com> wrote: > &g

Re: [gmx-users] uninstall gromacs 5.0

I am sorry for so many e-mails but check this link: http://installion.co.uk/ubuntu/vivid/universe/g/gromacs/uninstall/index.html Sent from my iPhone > On 23-May-2016, at 9:49 pm, Mark Abraham <mark.j.abra...@gmail.com> wrote: > > Hi, > > sun, that is not the name of any

Re: [gmx-users] uninstall gromacs 5.0

Running make uninstall also works Sent from my iPhone > On 23-May-2016, at 9:49 pm, Mark Abraham <mark.j.abra...@gmail.com> wrote: > > Hi, > > sun, that is not the name of any apt-supported GROMACS package that I know > of... > > Mark > >> On

[gmx-users] Deprotonated Asp and Glu

Hello I have simulated a protein ligand complex and analyzed the trajectory. After visualization of time frames and clusters.pdb; It occurs to me that the Asp and Glu are nit deprotonated although during pdb2gmx I used -inter command and deprotonated both residue according to pH 7. Can anyone

Re: [gmx-users] Deprotonated Asp and Glu

e > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of sun > <sun.i...@gmail.com> > Sent: Tuesday, May 24, 2016 8:33 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Deprotonated Asp and Glu > > The charge on Asp amd Glu seems 0 and hydrogens ar

Re: [gmx-users] Deprotonated Asp and Glu

The charge on Asp amd Glu seems 0 and hydrogens are present in time frames and cluster.pdb. But I deprotonated during pd2gmx. Sent from my iPhone > On 24-May-2016, at 6:00 pm, sun <sun.i...@gmail.com> wrote: > > Hello > I have simulated a protein ligand complex and analy

[gmx-users] PCA and FEL

Hello everyone I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis for the stability of my pro-lig complex. In a 2015 paper, The group calculated two principal component, PC1 and PC2 and then prepared an.xvg file to be used as input for g_sham. My question is, when we use

Re: [gmx-users] PCA and FEL

larity. So these order parameters > will be correlated. > > Cheers, > > Tsjerk > >> On Sun, May 15, 2016 at 8:13 AM, sun <sun.i...@gmail.com> wrote: >> >> Thank you very much Sir. I get you. Is it good enough to probe the >> stability of complex by projecting any tw

Re: [gmx-users] How to visualize the Free Energy Landscape file generated by g_sham

You can convert xpm2txt and plot in Origin as well Sent from my iPhone > On 29-Jan-2014, at 11:21 am, tarak karmakar wrote: > > Hi Monoj, > > You can use GNU 3D plot for this particular case. > > cheers, > Tarak > > > On Wed, Jan 29, 2014 at 8:02 AM, Monoj Mon Kalita

Re: [gmx-users] PCA and FEL

'^[@#]' proj1.xvg) <(proj2.xvg) | awk '{print $2, $4}' > > combined.xvg > > You will loose the labels, but that should be fine. > > You can combine other variables in a similar manner. > > Hope it helps, > > Tsjerk > >> On Sun, May 15, 2016 at 5:33 AM

[gmx-users] Supercomputing facility

Hello Users and experts We are going to create an account for a supercomputing facility. They have asked to fill a form to initiate the process. I am confused about certain terms as I belong to biology background. Please help me with these specific terms and what should I fill in to get good

Re: [gmx-users] Supercomputing facility

is not paid for). > > I hope it helps > > Andre > > >> On Thu, Jul 14, 2016 at 3:19 PM, sun <sun.i...@gmail.com> wrote: >> >> Hello Users and experts >> >> We are going to create an account for a supercomputing facility. They have >

Re: [gmx-users] PCA and gmx analyze

remarks about it before. > > Cheers, > > Tsjerk >> On Jun 27, 2016 1:11 PM, "Sun Iba" <sun.i...@gmail.com> wrote: >> >> Hello Users and experts >> >> My system details: >> Force field: GROMOS 43a1 >> >> Gromacs version:

Re: [gmx-users] Ligand hybridization

Use ATB for sure. PRODRG co-ordinates, charges are highly doubtful. I have prepared my ligand's topology using PRODRG and it took me almost 10 days to correct the charges. ATB is pretty good. Sent from my iPhone > On 05-Jul-2016, at 10:26 pm, Justin Lemkul wrote: > > > >>

Re: [gmx-users] Autocorrelation function

Allright. Thank you. Sent from my iPhone > On 01-Jul-2016, at 3:37 pm, Mark Abraham <mark.j.abra...@gmail.com> wrote: > > Hi, > > If an autocorrelation time is 7ps and you collect data every 20ps, can you > observe the former correctly? > > Mark > >&

[gmx-users] Autocorrelation function

Hello I have completed a protein ligand MD using Gromos43a1 and Gromacs v 5.0. I want to know while using gmx analyze, autocorrelation graph between eigenvectors is generated. However, the value is going sharply down to 0 and then to negative values. This probably means that something is wrong

Re: [gmx-users] protein has broken after 100ns simulation

Have you tried pbc nojump or whole with trjconv? Sent from my iPhone > On 02-Jul-2016, at 11:46 am, Seera Suryanarayana wrote: > > Dear gromacs users, > > I have simulated protein for 100ns. When I visualized the protein in VMD, I > have seen the protein into different

[gmx-users] virtual site independent from other structure

Hello everyone, I would like to create a virtual site which is independent from other structure. Is this possible? Best regards, Linlin Sun -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post

Re: [gmx-users] Atom type SDMSO not found

Here is the generated topology of ligand with PRODRG server, i believe something is wrong with atom typs here; PRODRG COORDS 29 1UNK CLAW 1 1.328 -0.638 -0.151 1UNK CAM 2 1.384 -0.765 -0.049 1UNK SAU 3 1.520 -0.861 -0.089 1UNK CAG 4 1.503

[gmx-users] LINCS WARNING

Hello Everyone I am simulation a protein as per the lysozyme tutorial. MY simulation got dumped at final mdrun step. It is showing following warning : Command line: gmx mdrun -deffnm md_0_1 Reading file md_0_1.tpr, VERSION 5.0.5 (single precision) Using 1 MPI thread Using 4 OpenMP threads

Re: [gmx-users] Water removed from system and visualizing protein alone in VMD. But problem in visualization of all frames (sun)

Thank You very much :) Regards Suniba On Fri, Feb 5, 2016 at 4:00 AM, Björn Sommer wrote: > Hello Everyone >> I have performed a md simulation if protein in water for 10ns and frames >> were obtained after every 10ps. I wanted to visualize the.gro and >> trajectory

Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

b or similar to > > get the plots automatically. But my question is if there is somewhere a > > repository of gromacs scripts with a script doing an analysis of the > > protein-ligand itneractions during trajectory. I do not think to be the > > only one requesting this > > > > >

Re: [gmx-users] Error: not enough memory

Allright I installed from source. Will do it again. Thank you very much NIkhil, once again. On Tue, Mar 22, 2016 at 11:35 AM, Nikhil Maroli wrote: > Hi, > this is problem regarding g_mmpbsa > > your not provided required information such as Gromacs version and > g_mmpbsa >

[gmx-users] Error: not enough memory

Dear Gromacs users I am doing an mm_pbsa analysis of my protein-ligand complex. I installed and it was nicely running on my workstation Z820. However, on a similar system, i installed using same steps but it is giving following error: *Not enough memory. Failed to calloc -1082130432 elements of

Re: [gmx-users] Extending the simulation

Thank you very much. Regards Suniba On Mon, Mar 7, 2016 at 10:09 AM, Nikhil Maroli wrote: > http://www.gromacs.org/Documentation/How-tos/Extending_Simulations > > -- > Gromacs Users mailing list > > * Please search the archive at >

Re: [gmx-users] Catenation and Visualization

Hello Tsjerk Thank you for your response. I have applied periodic boundary conditions and have loaded only one file i.e. movie.pdb in Pymol. Thats correct I can turn visualization off but my question is why two objects are showing up when I have catenated two trajectories. That's I asked if used

Re: [gmx-users] Hydrophobic interaction analysis

hi Its hydrophobic effect, Nikhil. And you can make index of hydrophobic groups in your protein, then calculate distance between them. On Thu, May 12, 2016 at 11:03 PM, Nikhil Maroli wrote: > Dear all, > > is there any option in gromacs to study the hydrophobic interaction

[gmx-users] Free energy landscpae

Hello users and experts I have performed a protein-ligand simulation with Gromos 43a1 ff and SPC water model. I performed PCA and selected first 2 principal components for construction of FEL using gmx sham. However, from the available references i have seen that the there exist both positive and

[gmx-users] Time frames missing

Hello everyone I have extended a 100 ns simulation of a protein in water up to 200 ns. However, the system kept shutting down during the course of simulation and i had to restart the runs twice. Following are the files I obtained after completion of mdrun (I am writing information of .xtc only,

[gmx-users] PCA and gmx analyze

Hello Users and experts My system details: Force field: GROMOS 43a1 Gromacs version: 5.0 OS: Ubuntu 14.0 Simulation time: 200 ns No. of eigenvectors and eigenvalues in gmx covar and gmx anaeig: 378 Protein backbone was used for least square fit and covariance analysis. I am trying to monitor

Re: [gmx-users] Free energy calculation, Methane in water tutorial

The single code from script reproduced the same error: C *ommand line: gmx grompp -f /home/Documents/tutorial/MDP/EM/em_steep.mdp -c /home/Documents/tutorial/Methane/methane_water.gro -p /home/Documents/tutorial/Methane/topol.top -o

Re: [gmx-users] Free energy calculation, Methane in water tutorial

The single code from script reproduced the same error: C *ommand line: gmx grompp -f /home/Documents/tutorial/MDP/EM/em_steep.mdp -c /home/Documents/tutorial/Methane/methane_water.gro -p /home/Documents/tutorial/Methane/topol.top -o

[gmx-users] Free energy calculation, Methane in water tutorial

Hello dear users I am following Justin's tutorial for free energy calculation of Methane in water. I have downloaded the job.sh file and trying to run it in terminal using: sh job.sh but it is giving following error: Program mdrun, VERSION 5.0 Source code file:

[gmx-users] Small molecule parametrization

Hi I have parametreized my small molecule with the help of ATB server. I have learnt that ATB provides GROMOS charges better than PRODRG. However, I have serious doubts regarding the charges assigned to hydrophobic groups. Also I need to convert the calculated charges into GROMOS 43a1 set (force

[gmx-users] ATB parametrization of small molecule

Hello everyone I want to simulate a protein ligand docked complex using GROMOS96 43a1 force field. I have prepared the ligand topology using ATB server. However, I want to know how can I validate the results of ATB when no experimental or computational data is available for small molecule. I have

Re: [gmx-users] Small molecule parametrization

x-us...@gromacs.org > Cc: > Subject: Re: [gmx-users] Small molecule parametrization > > > > On 9/7/16 1:43 PM, Sun Iba wrote: > > Hi > > I have parametreized my small molecule with the help of ATB server. I > have > > learnt that ATB provides GROMOS charg

[gmx-users] Catenation of trajectories

Hello everyonw I was wondering if it is possible to catenate multiple trajectories of same time-step and simulation length into one. Will it over write the information? For example I have five 50 ns trajectories of protein (time frames saved at 10 ps interval). The input .pdb file for second 50

Re: [gmx-users] Hydrophobic interaction energy

How would you define hydrophobic energy? I mean I have heard of hydrophobic effect that arises due to solvent but this term is new to me. You can calculate van der Waal term with MM-PBSA etc. People use this energy term to highlight the role of hydrophobic and non-polar amino acid residues towards

Re: [gmx-users] mpirun error

Thank you very much Andrew On Wed, Oct 19, 2016 at 10:31 AM, Andrew Guy <andrew@burnet.edu.au> wrote: > Hi Sun, > > In GROMACS 5.1, all the commands are under the gmx binary. You need to run > something like: > > >> source /your/installation/prefix/here/bin/GMX

[gmx-users] mpirun error

Dear Gromacs users and experts I am trying to run a test job of 1 ns remotely on supercomputer clusters. I have prepared .tpr file in my system (v 5.1.1) and submitted the script file on remote server. following is my script file:

[gmx-users] golp-CHARMM

Hi everyoneI want to simulate carboxylic acid self-assembled monolayer on a goldsurface with Golp-charmm parameters for Au(111) in Aqueous environment.[ref: J. Chem. Theory Comput. 2013, 9, 1616−1630].GolP-CHARMM parameters forthe Au(111) surface are presented in Table 2:  Surfacea            

[gmx-users] Gmx saxs [Error: atom (AL1) not in the list (26 types checked) !]

Hello, When I tried to calculate the structure factor of a clay using gmx saxs, I got the error :  Error: atom (AL1) not in the list (26 types checked) !  Clayff  force field is used in the simulation. Can anyone tell me what's the reason behind this error and how to fix it?Thanks! W. --

[gmx-users] how to visualize gromacs trajectory

Dear all, I wish to know what is the best way to visualize gromacs trajectory. When I load a gromacs trajectory into VMD, I find some of the water molecules and some part of the protein in the system are streched and the structure become weild and cannot be properly analyzed. I searched google

Re: [gmx-users] How to create a group for a set of atoms with make_ndx

got it. Thank you all for your help. On Fri, Aug 16, 2019 at 12:40 PM Bratin Kumar Das < 177cy500.bra...@nitk.edu.in> wrote: > Hi.. > The command is given below > gmx make_ndx -f *.gro -o *.ndx > You need to see inside the gro file what are the residue index > corresponding to the particular

Re: [gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory?

, and find the one with the smallest rmsd. But how to calculate the rmsd? The simulated structure has different atom number with the reference structure, so gmx rmsd wouldn't work. Do you know which method can work in this case? Best wishes. Yeping Sun On Mon, Aug 19, 2019 at 6:59 PM Justin

[gmx-users] How to prepare prm and itp files of ligands from gro and top files prepared with Gauss, ambertool and acpye for gromacs simulations

Dear everyone, In order to perform gromacs simulations with ligand-protein complex, I have to prepare the force field files for the ligand. I first use Gauss to generate a Lig.gesp file which describe the electrostatic potential. Then I use antechamber from ambertool to fit the gesp charges and

Re: [gmx-users] What is the "gen-vel" used for?

Hello Justin, Your reply is very helpful. I can understand the first method for proving repeatablity: use a different initial configuration. But how to set the different initial velocities with the same initial configuration if not using the "gen-vel" option in the .mdp file for the production

Re: [gmx-users] What is the "gen-vel" used for?

On Tue, Dec 31, 2019 at 12:22 PM Justin Lemkul wrote: > > > On 12/30/19 11:11 PM, sunyeping wrote: > > Hello Justin, > > > > Thank you for your reply. > > > > If I need to prove the repeatability of a phenonmenon (such as the > > peptide folding pathway or a conformational transition) in > >

Re: [gmx-users] What is the "gen-vel" used for?

for the three configurations respectively to get three independent trajectories? Best regards, Yeping On Fri, Jan 3, 2020 at 9:50 AM Justin Lemkul wrote: > > > On 1/2/20 8:25 PM, Sun Yeping wrote: > > Hello Justin, > > > > Your reply is very helpful. I can

[gmx-users] FEL - Invitation to view

I've shared an item with you: FEL https://drive.google.com/folderview?id=0Bw28I4GTBqd-cDVyWjRaSVd0Qms=sharing=COKa2skJ=5798ff47 It's not an attachment -- it's stored online. To open this item, just click the link above. -- Gromacs Users mailing list * Please search the archive at