Re: [gmx-users] Lipidbook webpage is off - is it possible to find its content somewhere?

Den 2019-12-04 kl. 01:21, skrev Oliver Beckstein: Hi Daniel, We had technical issues with the “server” that Lipidbook was running on (an old ~2006 MacMini…). We are in the process of moving it to a more reliable platform. However, that hasn’t been easy so it’s been dragging on for too long.

[gmx-users] Problem with GROMAC 2019.4

Hi all, I've been trying to get GROMAC 2019.4 to work on my computer with GPU acceleration for over 2 weeks, without success and without trying to bother you all here. Scouring the archives, someone else had the same exact issue I have (

Re: [gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer

Dear Justin, Thank you very much for your kind response. Best regards, Mijiddorj > -- > > Message: 6 > Date: Tue, 3 Dec 2019 10:54:48 -0500 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Charmm27 and Charmm36 atomtypes assignments >

Re: [gmx-users] gmx clustsize

It shows the time evolution of cluster size or aggregate size in the simulation...you need to provide one cutoff ...so that...when a atom or molecule cross the distance cutoff ...it considered to be the part of the aggregate...you can do gmx clustsize -h for further information. On Wed 4 Dec,

[gmx-users] Overriding atom type.

Hello Users, I was trying to run grompp for a membrane protein - ligand dynamics. I am using 4 5 ligands together. Under grompp run I got error overriding atomtype HGP1. Came out two ligands were sharing similar naming in atomtype section. I wanted to ask is it harmless to change it manually are

[gmx-users] gmx clustsize

Dear users, How gmx_clustsize algorithm works? Could you please help me. Thank you, Anand Sharma, Department of Biotechnology, IIT Madras (India)-600036 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] Fatal Error: cudaFuncGetAttributes failed

Hi, I've been getting this error repeatedly when running GROMACS on a cluster: --- Program: mdrun_mpi, version 2019.4 Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 100) MPI rank:0 (out of 6) Fatal error: cudaFuncGetAttributes

[gmx-users] Error: Atoms in the .top are not numbered consecutively

Dear All, I am gromacs beginner and I have gone through the Justing Lemku tutorial for KALP_15 in DPPC. I have reach the step three and trying to solve the error. The command line is: $ gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o

Re: [gmx-users] Lipidbook webpage is off - is it possible to find its content somewhere?

Hi Daniel, We had technical issues with the “server” that Lipidbook was running on (an old ~2006 MacMini…). We are in the process of moving it to a more reliable platform. However, that hasn’t been easy so it’s been dragging on for too long. However, I am happy to say that we are currently

[gmx-users] Lipidbook webpage is off - is it possible to find its content somewhere?

Every now and than I came across reference to, so called "lipidbook" ( https://lipidbook.bioch.ox.ac.uk/ ), which, as stated, contains force field parameters for various lipids.But webpage is obviously off for a long time, so I never have an opportunity to see its content. Moreover it looks very

Re: [gmx-users] solvent evaporation modeling

Hi Sako I did something similar where I dehydrated a system of water molecules, in my case a crystal but the principles are the same. I have uploaded the script at https://github.com/aslarsen/gromacs_dehydration/blob/master/gromacs_dehydration_MPI_V2.py It was used in this paper

Re: [gmx-users] Gromacs 2019.4 - cudaStreamSynchronize failed issue

Hi, I've run 30 tests with the -notunepme option. I got the following error from one of them(which is still the same *cudaStreamSynchronize failed* error): ``` DD step 1422999 vol min/aver 0.639 load imb.: force 1.1% pme mesh/force 1.079 Step Time 1423000

Re: [gmx-users] solvent evaporation modeling

Dear Sako, Unfortunately I don't have access to the script in the present since I'm in the middle of a travel. But anyway it was done in a specific way for the system that we were working on that time and would need some changes to work with different systems. I can describe to you the general

Re: [gmx-users] The total charge is not integer : -0.00465

On 12/3/19 3:59 PM, SAKO MIRZAIE wrote: Hi All, I did some MD studies on a protein: polymer system. After running grompp, it said, "the total charge is not an integer". the total charge is -0.00465. Can I continue the MD by adding -maxwarn flag? or it will be a problem and I will get

[gmx-users] The total charge is not integer : -0.00465

Hi All, I did some MD studies on a protein: polymer system. After running grompp, it said, "the total charge is not an integer". the total charge is -0.00465. Can I continue the MD by adding -maxwarn flag? or it will be a problem and I will get unrealistic results? Best, --

Re: [gmx-users] amide-capped C-terminus; OPLS force field

On 12/3/19 11:25 AM, Sahil Lall wrote: Hi, You need to add ions in the system to neautralise. and i think -0.18 qtotal considered as zero. That is absolutely not the case. Rounding errors should never amount to 0.001 or even less. Thank you for clarifying that Justin, that is what I

Re: [gmx-users] amide-capped C-terminus; OPLS force field

Hi, >> You need to add ions in the system to neautralise. >> >> and i think -0.18 qtotal considered as zero. > > That is absolutely not the case. Rounding errors should never amount to 0.001 > or even less. Thank you for clarifying that Justin, that is what I also thought too > If the OP is

Re: [gmx-users] Two atom oscillational period less than the time step

On 12/3/19 8:20 AM, Nikhil Maroli wrote: This may be due to the overlapping of the atoms or bad initial structure. The estimate of the oscillation period comes directly from the computed frequency of the bond from k_b. It has nothing to do with the coordinates. -Justin --

Re: [gmx-users] amide-capped C-terminus; OPLS force field

On 12/3/19 8:19 AM, Nikhil Maroli wrote: You need to add ions in the system to neautralise. and i think -0.18 qtotal considered as zero. That is absolutely not the case. Rounding errors should never amount to 0.001 or even less. If the OP is looking at charges in ffnonbonded.itp, those

Re: [gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer

On 12/1/19 5:43 PM, Mijiddorj B wrote: Dear Justin, Thank you very much for your response. I copied the ITP file that generated Charmm-gui. I am sorry for copied this long residue topology. The residue contains two capping groups that belong to first six atoms and the last six atoms. I

Re: [gmx-users] energy minimisation error

On 12/2/19 10:06 AM, Ayesha Fatima wrote: Dear All, Good morning. I am doing the Protein Ligand complex simulation tutorial from the Gromacs website. I followed the tutorial without any issue. When I want to run the energy minimisation md, i get the error message Are you working through

[gmx-users] Third beta release of GROMACS 2020

Hi GROMACS users, The third and final beta release of GROMACS 2020 is now out and available! As before, we are making the testing versions available for you to be able to get feedback on how well things are working, and what could be improved or if there are any bugs in the code we have

[gmx-users] Potential or total energy in dhdl files

Dear gromacs team, you wrote in documentation "This information is needed for later free energy analysis if the states of interest are at different temperatures. If all states are at the same temperature, this information is not needed. ‘potential’ is useful in case one is using mdrun -rerun to

Re: [gmx-users] npt.tpr protein-lig

Which forcefield and how did you made the topology for ligand? -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests

Re: [gmx-users] energy minimisation error

This is due to the bad initial structure. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -- 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] Two atom oscillational period less than the time step

This may be due to the overlapping of the atoms or bad initial structure. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For

Re: [gmx-users] amide-capped C-terminus; OPLS force field

You need to add ions in the system to neautralise. and i think -0.18 qtotal considered as zero. -- 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

[gmx-users] Pressure and restrains in NVT

Dear all, when using position restrains the pressure in NPT ensemble is only well defined when reference coordinates are scaled along with the system (refcoord-scaling=all). My question: Is the pressure well defined when I use position restrains in NVT? Or does the calculated pressure has

Re: [gmx-users] Disulphide bonded cyclic peptides

Hello, In the entries of the forcefied file *.rtp, *n.tdb and in *c.tdb. Yes I figured eventually that it was a stupid question to ask :) Thank you so much. On 2019-12-03 13:44, Alessandra Villa wrote: > Hi > > On Sat, Nov 30, 2019 at 2:04 PM Sahil Lall wrote: > > Thank you Alessandra.

Re: [gmx-users] Martini on GROMACS

Hello, All you need to run a Martini simulation is a gro file (most straightforward is to create an atomistic system and use martinize.py or generate lipids by insane.py) and a top file (fairly easy). After that you include the appropriate particle definition itp files in the working directory

Re: [gmx-users] Regarding LSI calculation

I tried by that. But i was suffering for making .xyz file for my system because I have lots number of frame around 8000. Can you tell me how can I make that kind of fu.XYZ . Thank you On Tue, Nov 19, 2019, 16:23 Christian Blau wrote: > Hi Omar, > > > Though I don't know of any GROMACS tool

Re: [gmx-users] Martini on GROMACS

Hi, In the tutorial I found only user instructions. I have GROMACS installed in central place for use of group, I did not find the installation instruction of Martini into GROMACS installation. Can someone direct me to the installation instruction? Thanks Shlomit On 27/11/2019, 15:56,

Re: [gmx-users] Two atom oscillational period less than the time step

Hi, On Tue, Dec 3, 2019 at 7:37 AM Mijiddorj B wrote: > Dear GMX users, > Hello, I would like to discuss the grompp message that tells the bonded > atoms oscillational period less than 10 times the time step. I am using > 0.002 ps time step. The choice of the time step depends on the force

Re: [gmx-users] Disulphide bonded cyclic peptides

Hi On Sat, Nov 30, 2019 at 2:04 PM Sahil Lall wrote: > Thank you Alessandra. > > I am extremely grateful for your help. It worked! > > However, one last bit > > You suggested to > > > use the one of the backbone > > for your new entry (since you do not have a real termini) for CYS-1 > > N