[gmx-users] position restraints for different protein atoms

Hi, Is there a way to generate position restraint files such that the main chain atoms and the side chain atoms have different force constants? Similarly, would it be possible to constrain atoms with B-factors lower than a certain threshold? Best, Irem -- Gromacs Users mailing list * Please

[gmx-users] fix COM

Dear Gromacs experts, Is there a approach to fix the centre of mass of a group of atoms only without fixing all of the atoms during a stretching process? Regards, Ming -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] Regarding Lipid bilayer genration (Bikash Ranjan Sahoo)

On 20/02/2016 1:02 pm, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Re: Regarding Lipid bilayer genration (Bikash RanjanSahoo) Just a remark: please note that you are free in the choice of the force field if you use the MembraneEditor. I used ffG45a3 and ffG53a6 without

Re: [gmx-users] Extend the simulation

Sorry Once, I added .tpr to the md_0_1 then it gave me the above message then I did as you said without .tpr. That error was obtained: Fatal error: Can't read 509132 bytes of 'md_0_1.log' to compute checksum. The file has been replaced or its contents have been modified. Cannot do appending

Re: [gmx-users] Extend the simulation

It says: No previous checkpoint file present, assuming this is a new run. Reading file md_0_1.tpr, VERSION 5.0.4 (single precision) Changing nstlist from 10 to 20, rlist from 1 to 1.03 then start.. /Elsaid On Sun, Feb 21, 2016 at 3:21 AM, Elsaid Younes wrote: > Ok, How

Re: [gmx-users] Extend the simulation

Hi, Please do exactly what Justin has suggested twice :-) Mark On Sun, 21 Feb 2016 02:21 Elsaid Younes wrote: > Ok, How can I use md_0_1.tpr instead of topol.tpr > > /Elsaid > > On Sun, Feb 21, 2016 at 2:59 AM, Elsaid Younes wrote: > > > Hi, > > > > The

Re: [gmx-users] Extend the simulation

On 2/20/16 8:21 PM, Elsaid Younes wrote: Ok, How can I use md_0_1.tpr instead of topol.tpr Your original command: gmx mdrun -deffnm md_0_1 "Run whatever mdrun you did before, but add -cpi -append." which means: gmx mdrun -deffnm md_0_1 -cpi -append -Justin /Elsaid On Sun, Feb 21,

Re: [gmx-users] Extend the simulation

Ok, How can I use md_0_1.tpr instead of topol.tpr /Elsaid On Sun, Feb 21, 2016 at 2:59 AM, Elsaid Younes wrote: > Hi, > > The mdrun I did was gmx mdrun -deffnm md_0_1 > I write the command > mdrun -cpi md_0_1_prev.cpt -append > I tried to use -noappend, but still doesn't

Re: [gmx-users] Extend the simulation

On 2/20/16 7:59 PM, Elsaid Younes wrote: Hi, The mdrun I did was gmx mdrun -deffnm md_0_1 I write the command mdrun -cpi md_0_1_prev.cpt -append I tried to use -noappend, but still doesn't work. To quote myself from my previous message: "Run whatever mdrun you did before, but add -cpi

Re: [gmx-users] Extend the simulation

Hi, The mdrun I did was gmx mdrun -deffnm md_0_1 I write the command mdrun -cpi md_0_1_prev.cpt -append I tried to use -noappend, but still doesn't work. /Elsaid On Sun, Feb 21, 2016 at 2:43 AM, Elsaid Younes wrote: > Still asks for topol.tpr? Can I have that file > > >

Re: [gmx-users] Extend the simulation

On 2/20/16 7:43 PM, Elsaid Younes wrote: Still asks for topol.tpr? Can I have that file You already have a .tpr file, otherwise your simulation never would have run. If you want help, you need to provide (1) the exact mdrun you gave originally for the job that stopped prematurely and (2)

Re: [gmx-users] Extend the simulation

Still asks for topol.tpr? Can I have that file /Elsaid On 2/20/16 6:49 PM, Elsaid Younes wrote: >* Hi, *>>>* If I have this file md_0_1_prev.cpt What is the text exactly? It asks *>* for topol.tpr * I gave you the command-line options that are new to the mdrun command line. Run whatever mdrun

Re: [gmx-users] Extend the simulation

On 2/20/16 6:49 PM, Elsaid Younes wrote: Hi, If I have this file md_0_1_prev.cpt What is the text exactly? It asks for topol.tpr I gave you the command-line options that are new to the mdrun command line. Run whatever mdrun you did before, but add -cpi -append. Doing this is a routine

Re: [gmx-users] Extend the simulation

Hi, If I have this file md_0_1_prev.cpt What is the text exactly? It asks for topol.tpr On 2/20/16 5:32 PM, Elsaid wrote: >* The simulation has the time, which is time of the wanted simulation. But the *>* job was killed by the server. * If the simulation terminated prior to completion, you

Re: [gmx-users] Extend the simulation

On 2/20/16 5:32 PM, Elsaid wrote: The simulation has the time, which is time of the wanted simulation. But the job was killed by the server. If the simulation terminated prior to completion, you don't need to operate on the .tpr file at all. Just continue from the last checkpoint mdrun

Re: [gmx-users] Extend the simulation

The simulation has the time, which is time of the wanted simulation. But the job was killed by the server. /Elsaid -- 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] Temperature Calculation in MD

On 2/20/16 3:58 PM, Ray Chao wrote: Hi, Justin, Thanks for your response. By extracting temperature information out edr file, do you mean the "gmx enemat" command? Actually what I was up to is No, you need gmx energy. calculate the temperature development of a certain region instead of a

Re: [gmx-users] Extend the simulation

Hi, You need to provide a number of ps by which you wish to extend, not the text "timetoextendby" Mark On Sat, 20 Feb 2016 21:55 Elsaid Younes wrote: > Hi all, > > I need to extend a previous simulation, and its directory is the same with > all inputs and outpts. That

Re: [gmx-users] Temperature Calculation in MD

Hi, Justin, Thanks for your response. By extracting temperature information out edr file, do you mean the "gmx enemat" command? Actually what I was up to is calculate the temperature development of a certain region instead of a group of atoms. -- Gromacs Users mailing list * Please search the

[gmx-users] Extend the simulation

Hi all, I need to extend a previous simulation, and its directory is the same with all inputs and outpts. That simulation can not be complete due to the maximum time of the job which is limited by the server. I use gromacs 5, when using the command gmx convert-tpr, an error is obtained. Command

Re: [gmx-users] Regarding Lipid bilayer genration (Bikash Ranjan Sahoo)

Hi Bikash, yeah, you can try CharmmGui. If it fails to create this small system, you can use our MembraneEditor with the Packing Algorithm Distributer and define the number of lipids you want to have. You will have to check which membrane size you want. Just check the are per lipid. Get

Re: [gmx-users] vacuum/gas md

On 2/20/16 1:49 PM, Rasha Alqus wrote: Dear Gromacs users, I have performed PMF calculation for my system in water at npt, I ran them on GPU . Now I wish to run them in gas phase and compare them with the waters and I have some questions: To run in gas I should place pbc=no

Re: [gmx-users] how to set Restraints

Please be sure to keep the discussion on the mailing list. On 2/20/16 8:54 AM, Sana Saeed wrote: thank you for explaining. i studied manual and understood restraints. but i don't know how to get phi dphi and other parameters, is there any formula or tool to get these values. phi = the value

Re: [gmx-users] converted topology from amber to gromacs

On 2/20/16 8:49 AM, mohammad r wrote: Hi Justin, Thank you for your answer, I used grompp and it didn't give me error. I've attached a topology file of my systems. Can you please take a look at this and tell me your opinion? You mean that it doesn't make any problem when after conversion

Re: [gmx-users] docking

On 2/20/16 7:03 AM, Negar Parvizi wrote: Hello friends, I want to dock a simulated protein like: human serum albumin to the drug. I was wondering if i could use docking with gromacs or other softwares?If I can use gromacs docking, where can i find a good tutorial ? GROMACS doesn't perform

Re: [gmx-users] Embedding Protein into lipid bilayer

Please don't spam the list with many copies of the same message. People give of their free time to answer questions on the list, so it may take a while for someone to respond. Please also make sure your emails are legible; yours are littered with bizarre characters. On 2/20/16 5:30 AM,

Re: [gmx-users] A questin to Justin on methods in the PPARγ-RXRα-DNA complex paper

On 2/20/16 1:59 AM, Timofey Tyugashev wrote: I was looking for examples of calculation setups. So I have a couple of questions about one used in this paper http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123984#sec008 Parameters are amber99sb-ildn and gaff: "Simulations were

Re: [gmx-users] REGRESSIONTESTS-5.1.tar.gz

Maybe try this one instead: https://github.com/gromacs/regressiontests/archive/release-5-1.zip Cheers, João On Sat, Feb 20, 2016 at 6:27 AM, ikrormi rungsung wrote: > Hi, > > I couldn't download REGRESSIONTESTS-5.1.tar.gz from this >

Re: [gmx-users] cutoff-scheme=Verlet

Hi, You might want to read this: http://www.gromacs.org/Documentation/Cut-off_schemes Basically, in the past Gromacs kept track of interactions through the group scheme (which made use of charge groups). The more recent verlet scheme doesn't use charge groups - that's what that line is telling

[gmx-users] cutoff-scheme=Verlet

Dear Gromacs user, In my NVT simulation, I user the Verlet as cutoff-scheme, but below note comes up in screen while .tpr generation; "Removing all charge groups because cutoff-scheme=Verlet" Does it mean that the atoms which I have indicated a charge for them in .top file will be removed? or

[gmx-users] docking

Hello friends, I want to dock a simulated protein like: human serum albumin to the drug. I was wondering if i could use docking with gromacs or other softwares?If I can use gromacs docking, where can i find a good tutorial ? thank you,Negar.Parvizi -- Gromacs Users mailing list * Please search

[gmx-users] A question to Justin about his helpful tutorial

pre.cjk { font-family: "Nimbus Mono L",monospace; }p { margin-bottom: 0.1in; line-height: 120%; }a:link { } Dear justin after finishing your tutorial, I tried to embed 1r2h protein into lipid bilayer. when I tried to use pdb2gmx� via "gmx pdb2gmx -f 2rh1.pdb -o

[gmx-users] Embedding Protein into lipid bilayer

Hi Catarina Thanks for your reply, I really appreciate it. you know, I complete Justins Tutorial, so I know what procedures I should do. but now I want to embed 2rh1 protein into DPPC lipid bilayer� which I already downloaded it from rcsb.com.� when I tried to use pdb2gmx�

[gmx-users] Embedding Protein into lipid bilayer

pre.cjk { font-family: "Nimbus Mono L",monospace; }p { margin-bottom: 0.1in; line-height: 120%; }a:link { } Hi Catarina Thanks for your reply, I really appreciate it. you know, I complete Justins Tutorial, so I know what procedures I should do. but now I want to embed 2rh1

Re: [gmx-users] Regarding Lipid bilayer genration

Hi Bikash, You can use a Charmm membrane with an Amber topology. The AA atom orders are the same, AFAIK. For what it's worth, you can generate membranes quickly using the coarse-grain command-line tool insane and (after equilibration) convert the result to AA with the backmapping tool backward.