Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 163, Issue 116

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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 163, Issue 116

> Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body

Re: [gmx-users] Umbrella sampling

Hello; I took 2000 configuration from trajconv. Amino acid is in its normal shape till almost conf1000.gro(and a little more). But in for example conf1300.gro amino acid was disintegrated. What does it mean? Would you please help me? Best regards Rose On Sun, Nov 26, 2017 at 12:39 AM, Justin

Re: [gmx-users] Not enough memory. Failed to realloc

Dear Justin It worked. Actually by its own. I reconstructed the pdb and gave again. Thank you so much for your time On Tue, Nov 28, 2017 at 10:08 AM, RAHUL SURESH wrote: > This error occur only for this particular pdb structure. The protein here > is attached with a

Re: [gmx-users] Not enough memory. Failed to realloc

This error occur only for this particular pdb structure. The protein here is attached with a metal ion. The necessary changes are made to the charmm36 ff. Should be some error in my pdb? On Tue, Nov 28, 2017 at 10:04 AM, RAHUL SURESH wrote: > Here i have added the

Re: [gmx-users] Not enough memory. Failed to realloc

Here i have added the report for the commands Command line: *gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c* Read 628 atoms Volume: 579.929 nm^3, corresponds to roughly 260900 electrons No velocities found system size : 3.716 91.693 1.702 (nm) diameter: 91.698

Re: [gmx-users] Fatal error in grompp

On 11/27/17 3:12 PM, Saumyak Mukherjee wrote: Dear Justin, Thanks for the reply. In that case, if I want the SOL-Backbone interaction energy, how shall I choose the energygrps? Is it possible to have such a group in the index.ndx file? You have to have fully intact charge groups, which

Re: [gmx-users] Fatal error in grompp

Dear Justin, Thanks for the reply. In that case, if I want the SOL-Backbone interaction energy, how shall I choose the energygrps? Is it possible to have such a group in the index.ndx file? Regards, Saumyak ‌ On 27 November 2017 at 19:05, Justin Lemkul wrote: > > > On

Re: [gmx-users] Build thin film.

Thank you :) On Sun, Nov 26, 2017 at 11:36 PM, Dallas Warren wrote: > You can do whatever you want, and there are many tools to help you do that. > > Couple of options are using gmx insert-molecules (constrain the box > size to make the film, then enlarge afterwards to

Re: [gmx-users] Not enough memory. Failed to realloc

On 11/27/17 11:26 AM, RAHUL SURESH wrote: Hi *gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c* And how large is the resulting box? Are all the coordinates properly defined? What is the full screen output of gmx solvate up to the failure? -Justin I have used the above command

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

On 26/11/17 17:08, Rakesh Pant wrote: Dear Alex, But g-x2top doesn't work till we define all atom types in .n2t file. Please do not use this at all. Use acpype or something. Thanks On 26-Nov-2017 9:34 PM, "Alexandr Nasedkin" wrote: Hi, You will need to have both

Re: [gmx-users] Performance test

Dear community, I share the results of scaling- performance test. I used this command and checked the core usage with the help of htop tool (http://hisham.hm/htop/): gmx mdrun -ntmpi 1 -ntomp N -pin on -deffnm & Where N is the number of (logical) cores, and hardware is Intel(R) Core(TM)

Re: [gmx-users] Not enough memory. Failed to realloc

Hi *gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c* I have used the above command to generate the box. Infact I have used this command before and I never got any error. Thank you On Mon, Nov 27, 2017 at 7:07 PM, Justin Lemkul wrote: > > > On 11/27/17 7:17 AM, RAHUL

Re: [gmx-users] pH dependent simulation

Thanks for correcting.. On Mon, Nov 27, 2017 at 7:02 PM, Justin Lemkul wrote: > > > On 11/27/17 1:02 AM, Tasneem Kausar wrote: > >> pKa of amino acid residue is a constant quantity. Depending on the pH you >> > > That's not strictly true. Titratable amino acids can be found

[gmx-users] SPC/Fw model of water

Dear Gromacs Users, I need the SPC/Fw model of water. Could I receive this model? Best Regards -- 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] Not enough memory. Failed to realloc

On 11/27/17 7:17 AM, RAHUL SURESH wrote: Dear Users I am trying to carryout protein-metal interaction using charmm36 ff. During solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o solv.gro" *i receive a error stating *"Fatal error:Not enough memory. Failed to realloc

Re: [gmx-users] Pdb2gmx melts molecules due to bad distances

On 11/27/17 6:04 AM, GIANMARCO BARTALINI wrote: Hello guys, I produced a system "protein + lipid membrane" using the online tool CHARMM-GUI. Since I need to use the Amber force field, I added the Lipids17 force field inside Gromacs. The implementation should work fine, since the conversion of

Re: [gmx-users] Fatal error in grompp

On 11/27/17 5:25 AM, Saumyak Mukherjee wrote: Dear All, I want to calculate the interaction energy between water and protein backbone. However, in mdp file, when I am using energygrps = SOL backbone ​grompp is returning the following error. Fatal error: atoms 1 and 2 in charge group 1 of

Re: [gmx-users] Pdb files generated on Lincs warning

On 11/27/17 1:04 AM, atb files wrote: Dear Users,When there is a Lincs warning (sometimes because of exceeding warnangle etc) the gromacs generates pdb files. My questions is:What is purpose of generating pdb files? What information they give? Which information

Re: [gmx-users] pH dependent simulation

On 11/27/17 1:02 AM, Tasneem Kausar wrote: pKa of amino acid residue is a constant quantity. Depending on the pH you That's not strictly true. Titratable amino acids can be found in unique microenvironments that cause shifts in canonical values. For instance, there are some catalytic

Re: [gmx-users] pH dependent simulation

On 11/26/17 11:09 PM, za...@tezu.ernet.in wrote: Hello Everyone I am trying to simulate a protein at two pH (7.4 and 9.0) using gromacs 5.1.4. The protein has no missing residues. Optimal pH range is 6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17 positively charged

[gmx-users] Not enough memory. Failed to realloc

Dear Users I am trying to carryout protein-metal interaction using charmm36 ff. During solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o solv.gro" *i receive a error stating *"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes for

[gmx-users] Pdb2gmx melts molecules due to bad distances

Hello guys, I produced a system "protein + lipid membrane" using the online tool CHARMM-GUI. Since I need to use the Amber force field, I added the Lipids17 force field inside Gromacs. The implementation should work fine, since the conversion of an equilibrated structure produces a nice and

Re: [gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan)

Dear Gerrit, Thank you very much for your prompt reply. I’ve tried to run the simulation with wenjin’s tutorial and it passed the point charge correction step with no problem. I compared the “.out” output files of my protein and of the tutorial peptide, I noticed there’s a line “%pointcharges

[gmx-users] Fatal error in grompp

Dear All, I want to calculate the interaction energy between water and protein backbone. However, in mdp file, when I am using energygrps = SOL backbone ​grompp is returning the following error. Fatal error: atoms 1 and 2 in charge group 1 of molecule type 'Protein_chain_A' are in different

Re: [gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan)

>From the error message it seems that ORCA program crashes. Unfortunately, Orca >is no longer supported, which means that if the ORCA's input or anything else >has changed, the gromacs interface may fail. What you could try is to use the version of ORCA that others have used before. Best,

Re: [gmx-users] Simulation on multi nodes performance

Hi, There's some useful background at http://manual.gromacs.org/documentation/2016.4/user-guide/mdrun-performance.html Whether you want mpirun -np X mdrun_mpi or mpirun -np X gmx_mpi mdrun depends whether GROMACS was configured to build only mdrun. Otherwise, the logfile is indeed your friend -

Re: [gmx-users] Simulation on multi nodes performance

On 27/11/2017 07:21, Ali Ahmed wrote:Hello GMX users I'm trying to do simulations on multi nodes so I used 8 nodes (128 processors). AS I see there is no difference between 1 node and 8 nodes. Check the log file showing how many nodes you use, look for a line as in template: Running on 2

[gmx-users] QM/MM-ORCA Point Charge Correction Error

Dear Gromacs Users, I've been running a QM/MM calculation on a protein with fluorescence probe, using gromacs 4.6.7 (double precision with MPI) and ORCA 4.0.1. The following lines were included in the .mdp file, QMMM = yes QMMM-grps= QMatoms QMmethod

[gmx-users] Pdb files generated on Lincs warning

Dear Users,When there is a Lincs warning (sometimes because of exceeding warnangle etc) the gromacs generates pdb files. My questions is:What is purpose of generating pdb files? What information they give? Which information we need to look for to analyse those