[gmx-users] Request for Plumed sample scripts

Hello everyone I am looking for a sample Gromacs script and a Plumed file with Distance Colvar. Please send me one if feasible. -- Cheers Peter -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] request

Hi, Please start by looking through the documentation, where many of these questions, and many more, are already answered. Mark On Tue, Apr 24, 2018 at 2:56 PM wrote: > What is the use of the neighbor list and can it be removed from mdp? > -- > This message has

[gmx-users] request

What is the use of the neighbor list and can it be removed from mdp? -- 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] request

when we use from verlet for neighbor list and why use from this, dont use from rlist in mdp file? -- 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] request

dose neighbor list to calculate rvdw and coulomb is necessary? -- 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] request

whats causes this error? Command line: gmx mdrun -s md_0_1 -cpi md_0_1.cpt Output file appending has been requested, but some output files listed in the checkpoint file md_0_1.cpt are not present or not named as the output files by the current program: Expect output files present: Expected

Re: [gmx-users] request

The error states what the problem is, there are three files that the program expects to be in the directory, but they aren't. Two things can do, change the command line if it is doing not what you want it to (i.e. it is trying to add more data onto an existing simulation, or you have used the

Re: [gmx-users] request

What is -s md ? in the command line. On 05-Dec-2017 12:32 AM, wrote: hi.what causes this error? Command line: gmx mdrun -s md -cpi md_0_1_prev.cpt Output file appending has been requested, but some output files listed in the checkpoint file md_0_1_prev.cpt are not

[gmx-users] request

hi.what causes this error? Command line: gmx mdrun -s md -cpi md_0_1_prev.cpt Output file appending has been requested, but some output files listed in the checkpoint file md_0_1_prev.cpt are not present or not named as the output files by the current program: Expect output files present:

[gmx-users] request

Command line: gmx mdrun -s md -cpi md_0_1_prev.cpt Output file appending has been requested, but some output files listed in the checkpoint file md_0_1_prev.cpt are not present or not named as the output files by the current program: Expect output files present: Expected output files not

[gmx-users] request

hi.what causes this error? Command line: gmx mdrun -s md -cpi md_0_1_prev.cpt Output file appending has been requested, but some output files listed in the checkpoint file md_0_1_prev.cpt are not present or not named as the output files by the current program: Expect output files present:

Re: [gmx-users] request

On 12/3/17 11:40 PM, mmahmou...@razi.tums.ac.ir wrote: hi. i have tpr file and cpt file but when i want doing restart for simulation with,gmx mdrun -s file.tpr -cpi file.cpt command I'm having trouble. please guide me With what? You need to be specific about the problem you're having in

Re: [gmx-users] Request to post to gromacs forun

On 01/10/17 17:38, Snijesh VP wrote: Hi Sir, It has been informed to email you to post my questions to the forum. Please do the needful You just did. -- "Work hard in silence let

[gmx-users] Request to post to gromacs forun

Hi Sir, It has been informed to email you to post my questions to the forum. Please do the needful -- "Work hard in silence let success make the noise" Snijesh VP Junior ​​

Re: [gmx-users] Request on initial velocities

Hi, The vv integrators write velocities on the full step, but those in the .tpr file are interpreted as occurring on the previous half step (which is consistent with how the leap-frog integrators start up). So a half-step of integration (ie. of velocities) takes place before any trajectory output

[gmx-users] Request on initial velocities

Dear Gromacs users, I am experiencing an issue in trying to perform a dynamics run by feeding in my own starting velocities. My procedure is as in the following: 1) I build my .gro file with the desired starting position and velocities; 2) I choose the flag "no" for the "gen-vel" option in the

[gmx-users] request

can you please email me and tell where i can see response to my question? thank you in advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Request for return of PDF containing all the commands, with help

On 9/17/14 6:02 PM, Dallas Warren wrote: Can I put in a request to have the full list of GROMACS commands/scripts, along with their help text, added back to the end of the manual? Or at least have a separate PDF available? What was the reason for removing that section? Over the years I

Re: [gmx-users] Request for return of PDF containing all the commands, with help

On Thu, Sep 18, 2014 at 12:02 AM, Dallas Warren dallas.war...@monash.edu wrote: Can I put in a request to have the full list of GROMACS commands/scripts, along with their help text, added back to the end of the manual? Or at least have a separate PDF available? I doubt it will come back in

Re: [gmx-users] Request for return of PDF containing all the commands, with help

Thank you Mark for the detailed response. Knew there had to be a good reason for it :) ... because the only way such documentation might stay up to date is to generate it from the code. We'd like to make the documentation Easier things are to do, more likely to stay up to date, and more time

[gmx-users] Request for return of PDF containing all the commands, with help

Can I put in a request to have the full list of GROMACS commands/scripts, along with their help text, added back to the end of the manual? Or at least have a separate PDF available? What was the reason for removing that section? Over the years I have found having them all there on screen, in