Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 2

-- Original -- From: "gromacs.org_gmx-users-request";; Date: Tue, Aug 1, 2017 07:16 AM To: "gromacs.org_gmx-users"; Subject: gromacs.org_gmx-users Digest, Vol 160,

[gmx-users] Some problem about the process of calculating MM-PBSA binding free energy

Dear users; I met some problem when I calculated the binding free energy between protein and ligand by the g_mmpbsa program. I am sure that I had read the tutorials of its official website and some other related information, but I don’t know what should I set the value of pconc or nconc in the

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 1

Dear Justin, Thank you very much. Best regards, Mijee > > -- > > Message: 4 > Date: Mon, 31 Jul 2017 18:47:12 -0400 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] gmx mdmat calculation of heavy atoms of two >

[gmx-users] Reg. Umbrella sampling problem with direction

Hello Everyone, I am novice in umbrella sampling. I did followed Dr. Justin's tutorial and it works fine for me. However, I would like to transport solute (along z-axis) from an ion channel (intracellular to extracellular site) so I made the system (Protein+solute+DPPC+Sol+ion) and came upto

Re: [gmx-users] ligand topology

Dear Sir Thank you very much for your reply. Can you give me any link or suggestion that i can learn for amber force field for protein and ligand. On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul wrote: > > > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote: > >> Dear Sir

[gmx-users] Question on Umbrella Sampling with varied ionic strength.

Hi all I have a question on umbrella sampling results under varied ionic strength. I have just done some regular umbrella sampling on the system of glucose 6-phosphate (small ligand molecule) on oligopeptide with LYS side chains. I mostly follow the tutorial by Justin

Re: [gmx-users] Question on Umbrella Sampling with varied ionic strength.

On 7/31/17 5:19 PM, Yuanchao Liu (MSU) wrote: Hi all I have a question on umbrella sampling results under varied ionic strength. I have just done some regular umbrella sampling on the system of glucose 6-phosphate (small ligand molecule) on oligopeptide with LYS side chains. I mostly follow

Re: [gmx-users] How can I implement a radial potential field in GROMACS?

On 7/31/17 1:07 PM, Wes Michaels wrote: Hello, (Cross-post from my original post here: https://www.researchgate.net/post/How_can_I_implement_a_radial_potential_field_in_a_MD_simulation_GROMACS) Is there a way to apply a potential field to all atoms in a simulation box in GROMACS? I'd like

Re: [gmx-users] gromacs rerun calculate the energy

On 7/31/17 8:03 AM, 王珍 wrote: Hi all, I used Gromacs run the biological system, which contains water, ions(Na+,Cl-), and nucleic. I used gromacs run the system, and the coulombtype was PME and the cutoff was 10 angstrom, then I want to use the commond rerun to calculate the

Re: [gmx-users] gmx mdmat calculation of heavy atoms of two side chains

On 7/31/17 1:19 AM, Мижээ Батсайхан wrote: Dear gmx users, I would like to know about the hydrophobic interaction between heavy atoms of side chains in different chains of peptides. How can I use mdmat tool for this calculation? I separately indexed all heavy atoms but mdmat use only one

Re: [gmx-users] hole in the simulation box

There are insufficient waters in the box to fill it up completely. Two solutions that come to mind, add more water so it reaches the appropriate simulated density under those conditions, or run under NPT until reaches appropriate simulated density then swap back to NVT. Catch ya, Dr. Dallas

[gmx-users] Question on Umbrella Sampling with varied ionic strength.

Hi all I have a question on umbrella sampling results under varied ionic strength. I have just done some regular umbrella sampling on the system of glucose 6-phosphate (small ligand molecule) on oligopeptide with LYS side chains. I mostly follow the tutorial by Justin

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

Hi, Did you get any warnings from grompp? Mark On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed wrote: > Hello GROMACS users, > > I'm doing MD for nitrogen, and for better electrostatic interactions I need > to use massless and charged virtual site. I did that but when I try to

[gmx-users] Hyper-threading on multi-CPU xeon worstation

Dear Gromacs users! I wonder to ask whether is possible to expect an increase in Gromacs performance with HT technology on my Xeon cpu (72 cpus without HT and 144 with HT)? How would be better to calibrate mdp options  (e.g integrator, adjust electrostatics cut-offs) to obtain best performance

[gmx-users] ligand topology

Dear Sir I am new for protein-ligand complex. I want amber force field (ff03) for my protein, tip3p for water model and gaff (General Amber force field) for ligand. I do not know how to produce gaff force field from pdb and then convert for gromacs topology. I have tried ff03 with gromos ligand

[gmx-users] How can I implement a radial potential field in GROMACS?

Hello, (Cross-post from my original post here: https://www.researchgate.net/post/How_can_I_implement_a_radial_potential_field_in_a_MD_simulation_GROMACS) Is there a way to apply a potential field to all atoms in a simulation box in GROMACS? I'd like to implement some radial potential energy

[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

Hello GROMACS users, I'm doing MD for nitrogen, and for better electrostatic interactions I need to use massless and charged virtual site. I did that but when I try to do energy minimization gives me LINCS warning and crush. I don't know where is the error I tried a lot but could not find a

Re: [gmx-users] Error in pdb2gmx

Hi, Google knows that better than I ;-) Mark On Mon, 31 Jul 2017 17:11 Souvik Dey wrote: > Can you name some of these softwares? I am relatively new in this. > > On Mon, Jul 31, 2017 at 4:59 PM, Mark Abraham > wrote: > > > Hi, > > > > You

Re: [gmx-users] Error in pdb2gmx

Can you name some of these softwares? I am relatively new in this. On Mon, Jul 31, 2017 at 4:59 PM, Mark Abraham wrote: > Hi, > > You need to build in the residue in a way that makes sense. Using some > other software, but there are some suggestions on the Gromacs

Re: [gmx-users] multiple cpu for g_membed job?

oh, I see. thx a lot On 07/31/2017 04:48 PM, Mark Abraham wrote: Hi, Only one rank, but I believe it works with the Verlet scheme and thus openmp and a single GPU. Mark -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Error in pdb2gmx

Hi, You need to build in the residue in a way that makes sense. Using some other software, but there are some suggestions on the Gromacs website. Mark On Mon, 31 Jul 2017 16:57 Souvik Dey wrote: > Hi, > > I am trying to run pdb2gmx on a long Amino Acid chain. However,

[gmx-users] Error in pdb2gmx

Hi, I am trying to run pdb2gmx on a long Amino Acid chain. However, one of the residues in the middle is incomplete. If I change the residue manually myself, would there be any problem in connectivity? Else, how do I sort out this problem? Souvik -- Souvik Dey Integrated Science Education &

Re: [gmx-users] multiple cpu for g_membed job?

Hi, Only one rank, but I believe it works with the Verlet scheme and thus openmp and a single GPU. Mark On Mon, 31 Jul 2017 16:44 Albert wrote: > Hi guys, > > Does anybody know whether g_membed support parallel running using > multiple CPU for a single job? > > thanks a

[gmx-users] multiple cpu for g_membed job?

Hi guys, Does anybody know whether g_membed support parallel running using multiple CPU for a single job? thanks a lot Albert -- 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] gromacs rerun calculate the energy

Hi all, I used Gromacs run the biological system, which contains water, ions(Na+,Cl-), and nucleic. I used gromacs run the system, and the coulombtype was PME and the cutoff was 10 angstrom, then I want to use the commond rerun to calculate the interaction of resid 1 and resid 2, I add

Re: [gmx-users] Creating Custom .rtp files

Hello, the .rtp file is located in the same directory as the force-field. When i type gmx gmx2pdb . then the log shows that the right path is considered and loads the needed .rtp fiels that already exist in the forc-field file. But my custom one is ignored. Greets Momin Ahmad Am

[gmx-users] Number of Clusters during my simulation

Hi all, I want to calculate the number of clusters of my glycine molecules during the course of my simulation. I have read that gmx clustsize is the correct command to use. I read on one of the previous threads that I will have create a separate tpr file for the molecule of interest. And I had

[gmx-users] Configuration of new HPC Cluster for GROMACS and NAMD

Hello everybody, I'm currently highly involved in the planning of a new HPC cluster for MD simulations. The main applications are GROMACS (sometimes in conjuction with PLUMED) and NAMD. Typical simulations are about 100,000 atoms up to 300,000 at max. So we got a quote from a manufacturer and

[gmx-users] Strange acceleration behaviour after continuation

Dear GMX users, I am trying to replicate a molecular flow of small molecules between two solid slabs of FCC bound atoms. The slabs are bound via LJ interactions.The flow is created by using periodicity, where the fluid is accelerated continuously between the two slabs. The periodic box is created

[gmx-users] Calculate RMSD between snapshots of two trajectories

Dear Gromacs Users, I would like to get a simple plot of RMSD versus time for two trajectories in *.gro format, where RMSD is calculated between structures at the same time, i.e. snap11 - snap12 snap21 - snap22 snap31 - snap32 snap41 - snap42 . . . where snap31 means third snapshot of the first

Re: [gmx-users] Nucleic Acid in GROMOS54A7

DA is the Adenine residue. It goes fine with other forcefields like CHARMM27 and AMBER99 SBILDN. In my knowledge, there's no problem in the parameters. Souparno Adhikary, CHPC Lab, Department of Microbiology, University of Calcutta. On Mon, Jul 31, 2017 at 3:43 PM, Mark Abraham

Re: [gmx-users] Nucleic Acid in GROMOS54A7

What is DA, and from your background knowledge of this force field, does it have suitable parameters or topologies for DA? Mark On Mon, 31 Jul 2017 11:02 Souparno Adhikary wrote: > Hi all, > > I was trying to simulate a protein-DNA complex using gromos54a7 forcefield. >

Re: [gmx-users] Using external force field with GROMACS

Hi, I don't understand your description of the problem, but you don't need to do anything with gmxlib in order to follow my solution, so make your life easy and do that. Mark On Mon, 31 Jul 2017 10:36 Souparno Adhikary wrote: > Hi, > > There's a new problem. Sysadmins

[gmx-users] Nucleic Acid in GROMOS54A7

Hi all, I was trying to simulate a protein-DNA complex using gromos54a7 forcefield. The error comes as, Fatal error: Residue 'DA' not found in residue topology database Clearly, it is not finding the DA residue in its database. How can I solve this? Thanks, Souparno Adhikary, CHPC Lab,

[gmx-users] (no subject)

Hi all, I was trying to simulate a protein-DNA complex using gromos54a7 forcefield. The error comes as, Fatal error: Residue 'DA' not found in residue topology database Clearly, it is not finding the DA residue in its database. How can I solve this? Thanks, Souparno Adhikary, CHPC Lab,

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 159, Issue 125

*Hi all,>> I am calculating the RDF from a particular residue to a particular> glycine molecule. I created an index file for both to do this. My> simulation box is 1.5nm, but the RDF values are in the range of 2nm-3nm.> I have viewed my trajectory and all the components stay inside the box.>

Re: [gmx-users] Using external force field with GROMACS

Hi, There's a new problem. Sysadmins installed the GROMACS 5.1.4 as a module in the cluster. We need to load it everytime we login as "module load gromacs-5.1.4". Now, if I mention GMXLIB path to the new forcefield files, the previous default installation of gromacs (4.5.6) points to it. How can

Re: [gmx-users] RDF Values

I think you can use -cut 0 -rmax 1.5 this will give you the RDF upto 1.5 nm.- Message from "Pandya, Akash" -     Date: Mon, 31 Jul 2017 07:29:19 +     From: "Pandya, Akash" Reply-To: gmx-us...@gromacs.org Subject:

[gmx-users] hole in the simulation box

Hi gromacs users, I am trying to simulate a crystal supershell (5x5x5 unit cells) with martini ff in gromacs 5. I build the system in aa representation, then I converted it in CG using the martinize.py script, following the tutorial, I've done a brief equilibration in water, the after the

Re: [gmx-users] RDF Values

hi dear!can anyone please suggest me what does it mean."In chosen Force field there is no residue type for QLN"there was no QLN in our origin file. There is always a problem when i select any force field.regards On Monday, 31 July 2017, 12:29, "Pandya, Akash"

[gmx-users] RDF Values

Hi all, I am calculating the RDF from a particular residue to a particular glycine molecule. I created an index file for both to do this. My simulation box is 1.5nm, but the RDF values are in the range of 2nm-3nm. I have viewed my trajectory and all the components stay inside the box. Please