[gmx-users] GROMACS/CPMD wavefunction optimize

Hi everyone,I'm trying to study on the damage of base by free hydroxyl radicals using GROMACS-CPMD program. However, error occurred in optimization of wave function. Would everyone tell me wheher the interface GMX and the OPTIMIZE option cannot be used at the same time? if permitted, How

[gmx-users] Reg. thread MPI errror with gromacs-2016.4

Hello experts,I ran a MD simulation on HPC where Gromacs-2016.4 installed on GPU.I run the production simulation using job file and it terminated with the fatal error: setting the number of thread-MPI ranks is only supported with thread-MPI and Gromacs was compiled without thread-MPI. Please

[gmx-users] Reg. thread MPI errror with gromacs-2016.4

Hello experts,I ran a MD simulation on HPC where Gromacs-2016.4 installed on GPU.I run the production simulation using job file and it terminated with the fatal error: setting the number of thread-MPI ranks is only supported with thread-MPI and Gromacs was compiled without thread-MPI. Please

[gmx-users] Surface Tension: equation and tail corrections?

Hello GROMACS users, I am using gromacs 2018.1 The manual and the gmx energy help page does not explicitly explain how the "(surface tension) x (surface number)" is calculated. I assume it is equation 3.69: L_{z} ( P_{zz}(t) - ( 0.5*P_{xx}(t) + 0.5*P_{yy}(t) ) ) Has anyone implemented a tool

[gmx-users] question about Gromacs 5.0.4 build

Hi all, I had installed Gromacs 5.0.4  on a Centos6 system a few years ago, and it was fine. We recently migrated our systems to Centos7, where Gromacs 2018 was installed, also without problems.  A user requested the old Gromacs 5.0.4 on the Centos7 system to complete a project. I worked

Re: [gmx-users] Position restrain in umbrella sampling

I checked it for each window. it just oscillates just for 0.1nm in each window and results are ok. I just asked to realize your main purpose ... And i'm convinced now ;) . Thank you for your kindly and detailed answers like always. Best regards -Rose On Wed, 6 Jun 2018, 20:01 Justin Lemkul,

Re: [gmx-users] [EXT] Re: Water in hydrophobic core of POPC lipid bilayer

On 6/6/18 11:38 AM, Smith, Iris wrote: Hi Dallas, Thank you so much for your expedient response. I increased the radius from 0.375 to 0.600 however upon solvation, the water filled the hydrophobic core again, albeit not as much as the initial solvation (at radius 0.375 added 6338 water

Re: [gmx-users] [EXT] Re: Water in hydrophobic core of POPC lipid bilayer

Hi Dallas, Thank you so much for your expedient response. I increased the radius from 0.375 to 0.600 however upon solvation, the water filled the hydrophobic core again, albeit not as much as the initial solvation (at radius 0.375 added 6338 water molecules; at radius 0.600 added 4672 water

Re: [gmx-users] Position restrain in umbrella sampling

On 6/6/18 11:18 AM, rose rahmani wrote: Hi, I'm doing umbrella sampling for different distances of amino acid from surface. I know that dear Justin warns people that position restraint was for that specific situation in the article mentioned in tutorial and I know it doesn't make a

Re: [gmx-users] Virtual sites causing npt simulation instabilities

On 6/6/18 11:13 AM, Eisenhart, Andrew (eisenhaw) wrote: new link with sole mdp file https://files.fm/u/cmyg863c This system doesn't even survive energy minimization for me, suggesting that the topology is not stable. The machine I'm on uses GROMACS 2016.3. Please upgrade to at least that

[gmx-users] Position restrain in umbrella sampling

Hi, I'm doing umbrella sampling for different distances of amino acid from surface. I know that dear Justin warns people that position restraint was for that specific situation in the article mentioned in tutorial and I know it doesn't make a sense in my system too in PULLING. But i don't

Re: [gmx-users] Virtual sites causing npt simulation instabilities

new link with sole mdp file https://files.fm/u/cmyg863c From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 9:30 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt

[gmx-users] What are SAsteps?

Hello all, I would like to perform a QM/MM simulation in gromacs, but when I run grompp, it asks for the value of SAsteps. I searched online for the meaning of this parameter and did not find anything. Can anyone please clarify what is the meaning of SAsteps, please? Thanks in advance and Best

Re: [gmx-users] g_trjorder output

On 6/6/18 5:47 AM, Apramita Chand wrote: Dear All, I want to choose a cutoff of 0.45nm and want to calculate the no. of urea molecules within 0.45 as well as beyond 0.45nm of the peptide backbone(for calculation of preferential interaction coefficient) I have a total of 18 urea molecules in

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 170, Issue 27

On 6/6/18 2:12 AM, Muthukumaran Rajagopalan wrote: thank you for the reply Justin. though the APL looks close to the acceptable range, I am afraid the SN1 and SN2 acyl chain parameters are not in the range as reported by Pluhackova, K et al J. Phys. Chem. B 2016, 120, 3888?3903 and also

Re: [gmx-users] Autocorrelation functions for distance vector

Den 2018-06-06 kl. 11:43, skrev Apramita Chand: Dear All, I want to calculate the time-dependent autocorrelation function for a peptide's end-to-end distance vector . If I use g_dist , it gives me a dist.xvg but though -lt option is there, the lifetime.xvg file is not generated. Is there any

[gmx-users] g_trjorder output

Dear All, I want to choose a cutoff of 0.45nm and want to calculate the no. of urea molecules within 0.45 as well as beyond 0.45nm of the peptide backbone(for calculation of preferential interaction coefficient) I have a total of 18 urea molecules in my system. I have tried the g_trjorder command

[gmx-users] Autocorrelation functions for distance vector

Dear All, I want to calculate the time-dependent autocorrelation function for a peptide's end-to-end distance vector . If I use g_dist , it gives me a dist.xvg but though -lt option is there, the lifetime.xvg file is not generated. Is there any command to calculate the autocorrelation function? (

Re: [gmx-users] Fwd: H2SO4 (H2PO4-) force field

I've tried to generate parameters for H2PO4 for Charmm in https://cgenff.paramchem.org/ and the results were pretty OK (at least in terms of penalties). Best Felipe On 06/06/18 10:22, Ondrej Kroutil wrote: Hi gromacs user, I have a favour to ask you. Does anybody have working model of

[gmx-users] Fwd: H2SO4 (H2PO4-) force field

Hi gromacs user, I have a favour to ask you. Does anybody have working model of sulfuric acid and/or H2PO4- (exactly these species with two OH groups)? I have tried to prepared one according to various articles: loukonen2010 - Enhancing effect of dimethylamine in sulfuric acid nucleation in the

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 170, Issue 27

thank you for the reply Justin. though the APL looks close to the acceptable range, I am afraid the SN1 and SN2 acyl chain parameters are not in the range as reported by Pluhackova, K et al J. Phys. Chem. B 2016, 120, 3888?3903 and also the membrane thickness increases. > > > > >

Re: [gmx-users] Charge groups in poly methyl methacrylic acid

Den 2018-06-06 kl. 05:01, skrev Debadutta Prusty: Hi everyone, I am new to gromacs and hence, this question might be naive. How does one go about assigning charge groups while creating new monomer topologies in .rtp files? What I gather from looking at similar posts is that the net charge of a