[gmx-users] Fw: EQUILIBRATION

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Hi Would you please help me how can i solve my problem ? I wanna to do equilibrate my complex ( 4ly1 + ligand) but when use the

Re: [gmx-users] Displacement of coordinates by an order of magnitude by pdb2gmx

The pdb file is in Angstroms. Gromacs uses nanometers, thus the decrease by a factor of 10 -> 1nm = 10A Peter -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Anna Lohning Sent: Friday,

[gmx-users] Displacement of coordinates by an order of magnitude by pdb2gmx

Hi I've looked all through the GROMACS documentation re actions of the PDB2GMX command but I cant' see a reference to why it appears to change the coordinates of the input .pdb file (basically decreasing them by an order of magnitude). Is this normal? When grepping out your docked ligands this

[gmx-users] Generating GROMACS input file from the GAMESS output file

Hi gmx users~ I would like to generate *.gro *itp file about one atom for MD simulation. So I calculated Fe metal atom using GAMESS program. -- FE.inp FE.dat FE.log -- How do I make GAMESS result file (.log) into AMBER

Re: [gmx-users] Fatal error: Invalid character in digit-only string: '�'

Yeah, Thanks for the clue. > -Original Messages- > From: "Mark Abraham" > Sent Time: Friday, July 7, 2017 > To: gmx-us...@gromacs.org > Cc: > Subject: Re: [gmx-users] Fatal error: Invalid character in digit-only string: > '�' > > Hi, > > Yes. And it looks

Re: [gmx-users] Fatal error: Invalid character in digit-only string: '�'

Hi, Yes. And it looks like you've copied and pasted a "smart quote" character produced from some fancy editor. If that's a tutorial or user guide, please ask them to fix it ;-) Mark On Thu, 6 Jul 2017 17:25 Hermann, Johannes wrote: > Hey Yu > > Try: > > gmx mdrun

Re: [gmx-users] Charge Mutation (State B) for Ions

Thank you very much, Justin! Best Johannes On 06.07.2017 14:43, Justin Lemkul wrote: On 7/6/17 8:42 AM, Hermann, Johannes wrote: Dear Justin, I think you were referring to amitabhjayas...@gmail.com Mails, right? You posted the link as answer to his question but now my object is in the

Re: [gmx-users] Fatal error: Invalid character in digit-only string: '�'

Hey Yu Try: gmx mdrun -v -ntmpi 8 -gpu_id -deffnm nvt So the same command you used, but _without_ the quotation marks. That is what the error tells you. Best Johannes On 06.07.2017 16:52, Du, Yu wrote: Dear Gromacs Users, I'm using the Gromacs 2016.3. I'm repeating the Tutorial 5:

[gmx-users] Fatal error: Invalid character in digit-only string: '�'

Dear Gromacs Users, I'm using the Gromacs 2016.3. I'm repeating the Tutorial 5: Protein-Ligand Complex. If I use `gmx mdrun -deffnm nvt`, Gromacs will not show any error. If gmx mdrun -quiet -nt 8 -ntomp 2 -gpu_id “” -deffnm nvt, I will get the following errors. Is this a bug or the

[gmx-users] ACCELERATE SIMULATION

HELLO, I had run simulation for my protein which has 1200 residues it took 10 days for 10 ns on simple mdrun command. I have a graphic card with the following configuration: VGA compatible controller: Advanc VGA compatible controller: Advanced Micro Devices, Inc. [AMD/ATI] Bonaire [FirePro

[gmx-users] User-defined Nonbonded Potentials and Cutoff Treatment

Hello all, I'm trying to systematically scale down the non-bonded interaction between two specific atom types without perturbing the interactions with the other species (basically multiplying their pair potential by 0

Re: [gmx-users] Doubt about Free Energy control Minimization

On 7/6/17 8:42 AM, Varvdekar Bhagyesh Rajendra wrote: Dear Justin, It would be helpful if you please explain in a bit more detail about the impact of the settings of table-extension. The manual says "Extension of the non-bonded potential lookup tables beyond the largest cut-off distance",

Re: [gmx-users] Charge Mutation (State B) for Ions

On 7/6/17 8:42 AM, Hermann, Johannes wrote: Dear Justin, I think you were referring to amitabhjayas...@gmail.com Mails, right? You posted the link as answer to his question but now my object is in the object line. Yes, because it was important to correct the record and because failing to

Re: [gmx-users] Doubt about Free Energy control Minimization

Dear Justin, It would be helpful if you please explain in a bit more detail about the impact of the settings of table-extension. The manual says "Extension of the non-bonded potential lookup tables beyond the largest cut-off distance", but a better insight from you would be definitely more

Re: [gmx-users] Charge Mutation (State B) for Ions

Dear Justin, I think you were referring to amitabhjayas...@gmail.com Mails, right? You posted the link as answer to his question but now my object is in the object line. However, I am still looking for an answer to my question. Is there anyone, who can tell me something about my dual

Re: [gmx-users] Acetonitrile with CHARMM ff

On 7/6/17 6:34 AM, Sonia Milena Aguilera Segura wrote: Dear Justin, Thank you for your reply. I went trough the CHARMM forum and I found this post of 2007, https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat=28545, which basically underlines the same issues I am having. I read

Re: [gmx-users] simulation at different temperature

On 7/6/17 1:15 AM, Alex Mathew wrote: Dear Justin, Thanks for the reply, Could you tell me what is the unique purpose of the REMD and where I can learn it from basics? A simple web search will come up with numerous review articles. The higher temperature replicas allow for more frequent

Re: [gmx-users] Charge Mutation (State B) for Ions

On 7/6/17 12:56 AM, amitabh jayaswal wrote: ... well, this URL under ans.2 (http://www.bevanlab.biochem. vt.edu/Pages/Personal/justin/gm) isn't working. 404 Not Found is what I'm repeatedly getting. Please rectify/improve. Because you haven't copied the whole URL, which is split across two

[gmx-users] How to convert two domains of prtoein into two beads by Conarse-grained Molecular Dynamics (CG-MD)?

Hello all How to convert multi-domain protein into single bead depending on the number of domains i.e. if a protein contains two domain. Then how to represent it into two beads for CG-MD. *How to convert two domains of prtoein into two beads by Conarse-grained Molecular Dynamics (CG-MD)?*. With

[gmx-users] How to convert two domains of prtoein into two beads by Conarse-grained Molecular Dynamics (CG-MD)?

Good evening all, How to convert multi-domain protein into single bead depending on the number of domains i.e. if a protein contains two domain. Then how to represent it into two beads for CG-MD. *How to convert two domains of prtoein into two beads by Conarse-grained Molecular Dynamics

Re: [gmx-users] Acetonitrile with CHARMM ff

Dear Justin, Thank you for your reply. I went trough the CHARMM forum and I found this post of 2007, https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat=28545, which basically underlines the same issues I am having. I read this post before posting here, and this why I came with the

Re: [gmx-users] re cant login to Gromacs User forum

Hi, Apologies, I meant that last email to go to Anna only. I've changed that password ;-) Mark On Thu, Jul 6, 2017 at 10:37 AM Mark Abraham wrote: > Hi Anna, > > I assume you meant logging into http://www.gromacs.org/. I made you an > account in the name

Re: [gmx-users] Fwd: Relative free energy perturbation

On Thu, 6 Jul 2017 09:17:18 +0200 Davide Bonanni wrote: > I am apologize if I resend the same message but I forgot to change the > object. > > Dear Hannes, > > Thank you very much for your reply, really appreciated. > > > > > Date: Mon, 26 Jun 2017 12:09:45 +0100 >

Re: [gmx-users] re cant login to Gromacs User forum

Hi Anna, I assume you meant logging into http://www.gromacs.org/. I made you an account in the name alohn...@bond.edu.au with password "gromacs." Please log in and change at least the password. If you meant something else, can you let me know? Mark On Thu, Jul 6, 2017 at 10:30 AM Anna Lohning

Re: [gmx-users] re cant login to Gromacs User forum

Hi Anna, I'm not sure what forum you're referring to. www.gromacs.org is currently under replacement, in part because such things do not work well and the infrastructure is out of supported lifetime. I'll contact you off-list for some details. Mark On Thu, Jul 6, 2017 at 10:30 AM Anna Lohning

[gmx-users] re cant login to Gromacs User forum

Hi I'm having all kinds of trouble logging in to the Gromacs User Forum. I have registered but when I try to log in with my email (assuming this is my 'username') and password it says there's no user by that name. It's super frustrating. Is there a problem with the site? Would appreciate any

Re: [gmx-users] TIP4P/ice pdb file

Dear Chris, Yes, tip4p.gro worked well. Thank you On Wed, Jul 5, 2017 at 10:55 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the

Re: [gmx-users] Fwd: Relative free energy perturbation

I am apologize if I resend the same message but I forgot to change the object. Dear Hannes, Thank you very much for your reply, really appreciated. > Date: Mon, 26 Jun 2017 12:09:45 +0100 > From: Hannes Loeffler > To: >