Re: [gmx-users] How to remove the water molecules?

Hi Surya, Non-Water is a default index group. Just select that when running trjconv. Cheers, Tsjerk On Tue, May 12, 2015 at 8:34 AM, Seera Suryanarayana wrote: > Dear gromacs users > I have simulated a protein for 500ns in solvent system. I want to remove > water molecules from the system to

[gmx-users] How to remove the water molecules?

Dear gromacs users I have simulated a protein for 500ns in solvent system. I want to remove water molecules from the system to further analysis. I have gone through the manual, but I couldn't find how to remove water molecules. Kindly tell me how can I do it. Thanks in Advance Surya Graduate stude

Re: [gmx-users] all-atom pca

Hi Jio, No, the 'extreme structures' are filtered along the eigenvector and are not real structures. But you wanted the corresponding all-atom ones. Cheers, Tsjerk On May 12, 2015 00:45, "gromacs query" wrote: > Hi Tsjerk > > In -proj plot of v1 vs Time I used extreme values of V1 and saw stru

[gmx-users] question

Dear Justin Very thanks for your answer I should use my pdb file in which there is no bond between CD atom of GLU residue from peptide 1 and NZ atom of LYS residue from peptide 2. Creating new entry in specbond.dat file will consider this new bond. Is my vision true? Based on your answer, only t

[gmx-users] Dihedral copying from itp to ff

Dear User, I have done MD simulation successfully with ligand.itp file produced by Antechamber. Now I have to include the ff information of the ligand into AMBER99SB forcefield and in the process I am so for successful in creating rtp entry and bond and angles parameter in ffbonded.itp file but I h

Re: [gmx-users] LINCS warnings and ligand topology

Hi Justin, Thanks for your suggestions. >Hacking off atoms because the simulation fails is a pretty bad strategy :) Indeed, I removed all O atoms and S atom. Simulations in solvent are perfectly fine. This might suggest that the errors (warnings) came directly from these deleted atoms, especia

Re: [gmx-users] first residue in chains warning issue

Hi Justin, Here is the output of pdb2gmx: Command line: pdb2gmx -f hyp_lys.pdb -o complex.gro -ignh -ter -ff gromos54a7 -water SPC Using the Gromos54a7 force field in directory gromos54a7.ff Opening force field file /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.r2b Reading h

Re: [gmx-users] all-atom pca

Hi Tsjerk In -proj plot of v1 vs Time I used extreme values of V1 and saw structures on those times. When I compare these structures to the structures obtained from -extr the atomic positions (of 'same' extremes) are not 'exactly' matching even after fitting. I tried with double precision as well.

Re: [gmx-users] all-atom pca

Hi Jio, You'll have to look at the projections (-proj), and see at which time these have an extreme value. Cheers, Tsjerk On Mon, May 11, 2015 at 11:00 PM, gromacs query wrote: > Hi Tsjerk > > Thanks for reply. > > >> So you can use the times > I am unable to use it as explained below. > > I

Re: [gmx-users] all-atom pca

Hi Tsjerk Thanks for reply. >> So you can use the times I am unable to use it as explained below. I get extremes output pdb like this: g_covar -s avg.pdb -f all_frames.pdb g_anaeig -s avg.pdb -extr two_extremes.pdb -first 1 -last 1 -nframes 2 Visually two structures in two_extremes.pdb looks

Re: [gmx-users] all-atom pca

Hi Jio, The scores for all-atom structures will be strongly correlated to those for heavy-atom structures. So you can use the times for the heavy-atom extreme projections to extract all-atom structures. Cheers, Tsjerk On Mon, May 11, 2015 at 10:32 PM, gromacs query wrote: > Hi All > > I am do

Re: [gmx-users] question

On 5/11/15 2:34 PM, Andrew Bostick wrote: Dear gromacs users I have experience in MD simulation of protein and peptides by gromos force field. Now I am working on a new project in which I should connect two peptides (based on experimental data) to obtain one new peptide. This connection is as

Re: [gmx-users] LINCS warnings and ligand topology

On 5/11/15 2:24 PM, MPI wrote: Dear Users, I prepared ligand topologies by two different methods, one with Acpype and the other with Prodrg. It is sad that independent simulations give the same (or similar) numerous Lincs warnings and the system blew up at the end. Errors look like LINCS W

Re: [gmx-users] Giving an initial velocity to a group of atoms

On 5/11/15 11:03 AM, Jashimuddin Ashraf wrote: Thanks again for your reply Dr. Lemkul. I was also expecting a disaster because I gave an unrealistic starting velocity of the structure. But the simulation was running fine. I tried using the gmxdump and found that the velocities I am getting are

[gmx-users] all-atom pca

Hi All I am doing PCA and its working fine if I choose few atoms only (heavy) and I get extreme pdb file having heavy atoms for, say, eigenvector 1. But I want to have extremes of all-atom structures, so I thought of doing PCA on all-atoms but I end up with having Segmentation default error which

Re: [gmx-users] [PyMOL] how to connect to atoms?

Hi Leila, This too is more a question for the Gromacs mailing list. Gromacs does not read bond information (CONECT records) from a PDB file. It only reads the ATOM/HETATM records and sets bonds based on the force field building block definitions and the special bonds (such as the isopeptide link)

Re: [gmx-users] question

In fact, I want to make an isopeptide bond. On Mon, May 11, 2015 at 11:04 PM, Andrew Bostick wrote: > Dear gromacs users > > I have experience in MD simulation of protein and peptides by gromos force > field. > > Now I am working on a new project in which I should connect two peptides > (based o

[gmx-users] question

Dear gromacs users I have experience in MD simulation of protein and peptides by gromos force field. Now I am working on a new project in which I should connect two peptides (based on experimental data) to obtain one new peptide. This connection is as follows: CD atom of GLU residue from peptide

[gmx-users] LINCS warnings and ligand topology

Dear Users, I prepared ligand topologies by two different methods, one with Acpype and the other with Prodrg. It is sad that independent simulations give the same (or similar) numerous Lincs warnings and the system blew up at the end. Errors look like LINCS WARNING relative constraint deviatio

Re: [gmx-users] Giving an initial velocity to a group of atoms

Thanks again for your reply Dr. Lemkul. I was also expecting a disaster because I gave an unrealistic starting velocity of the structure. But the simulation was running fine. I tried using the gmxdump and found that the velocities I am getting are not the velocities I've given to the atoms. In yo

Re: [gmx-users] Gromacs 4.6.7 with MPI and OpenMP

Mark, On Friday 08 May 2015 15:15:31 Mark Abraham wrote: > > FWIW, I ran the same GROMACs run outside of the queuing system to verify > > that the CPUSETs were not causing the issue. > > > > MPI gets a chance to play with OMP_NUM_THREADS (and pinning!), too, so your > tests suggest the issue lie

Re: [gmx-users] Gromacs 4.6.7 with MPI and OpenMP

Szilárd, On Friday 08 May 2015 21:18:12 Szilárd Páll wrote: > >> What is your goal with using CPUSETs? Node sharing? > > > > Correct. While it might be possible to see the cores that have been > > assigned to the job and do the correct 'pin setting' it would probably be > > ugly. > > Not sure

Re: [gmx-users] implicit solvent concerns

Thanks for being so clear Mark. Best, Albert On 05/11/2015 03:18 PM, Mark Abraham wrote: Hi, Stuff was probably broken here before 4.6. I would trust only single threaded in 4.6 and later, and only after comparing with 4.5. Mark On Mon, 11 May 2015 14:50 Albert Solernou wrote: Hi All, I a

Re: [gmx-users] Subject: Re: how to avoid multiple 'aprun' on batch job script?

Hi, Please see http://www.gromacs.org/Documentation/How-tos/Extending_Simulations and try things out. We can't bless everybody's scripts... Mark On Mon, 11 May 2015 15:30 Satyabrata Das wrote: > Dear Dr. Mark Abraham, > Thank you for all the suggestions. > I have a query now about the 'mdrun'

Re: [gmx-users] implicit solvent concerns

Hi, Stuff was probably broken here before 4.6. I would trust only single threaded in 4.6 and later, and only after comparing with 4.5. Mark On Mon, 11 May 2015 14:50 Albert Solernou wrote: > Hi All, > I am thinking of running an implicit solvent simulation using Gromacs > (.mdp file pasted at

Re: [gmx-users] Subject: Re: how to avoid multiple 'aprun' on batch job script?

Dear Dr. Mark Abraham, Thank you for all the suggestions. I have a query now about the 'mdrun' restart command line: First run: export OMP_NUM_THREADS=2 aprun -n 144 -N 24 -j1 mdrun_mpi -npme 48 -maxh 24 -v -deffnm simu-100ns (simu-100ns.tpr for whole 100ns) Restart-1,2,3...etc: export OMP_NUM_TH

[gmx-users] implicit solvent concerns

Hi All, I am thinking of running an implicit solvent simulation using Gromacs (.mdp file pasted at the end of the email). However, I am a bit concerned about its accuracy as I get different results for the Polarisation term. More specifically, the first step of an energy minimisation gives dif

Re: [gmx-users] HYL force field

On 5/11/15 8:19 AM, Ming Tang wrote: Dear Justin, The protein contains 15 constituent HYL residue modified from LYS. I realized that I need to modify the .rtp, but have no idea about how to derive the parameters correctly. Do you have any suggestions for this? As I said, it depends on th

Re: [gmx-users] HYL force field

Dear Justin, The protein contains 15 constituent HYL residue modified from LYS. I realized that I need to modify the .rtp, but have no idea about how to derive the parameters correctly. Do you have any suggestions for this? thanks a lot. From: gromacs.o

Re: [gmx-users] Why h_bond can not form

It's so kind of you to answer my question in such a short time. I'll try other forcefields. Thank you very much! 在 2015-05-11 19:46:27，Justin Lemkul 写道： > > >On 5/10/15 8:48 PM, 范聪 wrote: >> Hello everyone! >> >> I offered a picture called "ask.png" to illistrate my question. >> >> According to

Re: [gmx-users] Harmonic COM Restraints with the Pull Code

On 5/9/15 9:52 PM, Eric Dybeck wrote: Hello All, I am looking to run a set of simulations in which molecules are slowly restrained to their COM positions. To provide some context, I am going to melt a solid, and I would like to restrain the molecules first so that they remain in their lattice

Re: [gmx-users] Why h_bond can not form

On 5/10/15 8:48 PM, 范聪 wrote: Hello everyone! I offered a picture called "ask.png" to illistrate my question. According to the referense papers, the H atom of the -OH group of TYR306 should form H_bond with the carbonyl O atom of the ligand. Depending on the methods used in those papers,

Re: [gmx-users] Sanjay (Re: Energy minimization problem)

On 5/10/15 3:28 PM, sanjay choubey wrote: HI,I am running membrane protein dynamics. After energy minimization i am getting the following error. I am not getting how to rectify it.Energy is minimized in fewer steps. Without proper minimization i cant proceed to next step of NVT run.

Re: [gmx-users] first residue in chains warning issue

On 5/10/15 11:36 PM, Ming Tang wrote: Dear all, I built a triple helix with 2 GLN and 1 SER being the first residue of the three chains. However, while using pdb2gmx -f 1.pdb -o complex.gro -ignh -ter -ff gromos54a7 -water SPC and choosing NH2 or NH3+ as the start terminus type for GLN-1 a

Re: [gmx-users] HYL force field

On 5/10/15 10:12 PM, Ming Tang wrote: Hi, 范聪 I have never worked with ligand, and will try to learn this tutorial. I think you need to define what "containing" means - is it a constituent residue of the protein sequence or is it a noncovalently bound ligand? The approach in both cases dif

Re: [gmx-users] Subject: Re: how to avoid multiple 'aprun' on batch job script?

Hi, You should check out the other recent discussion in this list on performance variation. Getting your GROMACS nodes allocated close together is an important part of mitigating such problems. Rather than manually splitting your job into small pieces, you can have mdrun do that automatically for

Re: [gmx-users] During mdrun my protein moves towards edges

You do not have a "problem" you only have the "normal" protein diffusion. Take a look in trjconv tool. http://manual.gromacs.org/programs/gmx-trjconv.html Option -center will be your best friend I guess. Diogo Vila-Viçosa Em seg, 11 de mai de 2015 às 10:14, Seera Suryanarayana escreveu: >

[gmx-users] During mdrun my protein moves towards edges

Dear gromacs users I have been running the real mdrun after equilibration. mdrun has been submitted for 500ns. After some time(150ns) the protein moves towards edges. I want the internal moments only, but whole protein moves all sides of box rather than at centre of the box. Kindly tell me how to