Re: [gmx-users] energy minimization

Gas phase simulations the inter-molecular interactions are smaller, and intra-molecular interactions dominate. Therefore total energy will be positive. If it was filled with a solvent i.e. liquid phase, then inter-molecular inteactions dominate and the total energy will be negative. Catch ya,

[gmx-users] energy minimization

hi friends I generated a box of mixed gas with gmx insert-moleculesI ran an energy minimizing.  the potential energy is 4.05e+07 and maximum force is 1.25e+03.I used different algorithm likes cg and steep for minimization. what do I have to do untill my system potential energy has negative

Re: [gmx-users] energy minimization in vacuum

Hi, If u minimise the protein in vaccum...the bad contact within the protein atoms will be removed After solvation if u do...then both the bad water contact and steric clashes within the protein will be removed. On Mon 16 Mar, 2020, 8:37 PM Deepanshi ., wrote: > Dear all, > > I am trying

[gmx-users] energy minimization in vacuum

Dear all, I am trying to simulate an all atom protein in water. I wanted to ask that what is the importance of minimizing the protein in a vacuum. It is not mentioned in the lysozyme tutorial. Thanks. Regards, Deepanshi -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Energy minimization

This all sounds like http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc Remember, the box is just a visualisation of what the system looks like, and you can move that box anywhere. What is in the center of the box is entirely up to you and the post processing you

[gmx-users] Energy minimization

Hello all, I created a graphene sheet and performed energy minimization, after energy minimization I found that parts of the graphene sheet was moved from the box bottom to the box topside at the same place (as if it was translated upwards). I looked online for the problem and I understood that I

[gmx-users] Energy minimization problem for POPE/POPG soluted bilayer taken from M. Karttunen website

Dear users I tried energy minimization of POPE/POPG bilayer from http://www.softsimu.net/downloads/pepg-mix.pdb . Process stopped and forces have not converged to requested precision (output shown below). I used Gromacs version 2019.2 . My colleague also used this bilayer before with earlier

Re: [gmx-users] energy minimization

Hi, Typical force fields will have negative energies at minimize configurations, but my guess is that your initial configuration has some serious problem. Did you visualise the minimization start and end points? Mark On Tue., 27 Aug. 2019, 18:52 Dhrubajyoti Maji, wrote: > Dear gromacs users,

[gmx-users] energy minimization

Dear gromacs users, I am doing energy minimization of a neat urea system. When I set emtol = 10 the following result is obtained : Steepest Descents converged to machine precision in 33995 steps, but did not reach the requested Fmax < 10. Potential Energy = 6.7910172e+04 Maximum force =

Re: [gmx-users] energy minimization

Look around atom 2016, there is a bad contact between the atoms in that area, hence the infinite force, very high potential energy, and the minimisation fails. On Tue, 25 Sep. 2018, 6:48 pm ikjk, <1761440...@qq.com> wrote: > hello >I am doing a md with martini force filed,I create a box,

[gmx-users] energy minimization

hello I am doing a md with martini force filed,I create a box, there is a double monolayer, then I solvate it, but when I did energy minimization, gmx grompp -f minim.mdp -c solv.gro -p dppc.top -o em.tpr then NOTE 1 [file minim.mdp]: With Verlet

Re: [gmx-users] energy minimization

on behalf of Justin Lemkul Sent: Wednesday, July 25, 2018 8:17 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization On 7/24/18 7:24 AM, farial tavakoli wrote: > Dear Justin > > I used LigParGen server to generate ligand topology but I dont know what > changes

Re: [gmx-users] energy minimization

On 7/24/18 7:24 AM, farial tavakoli wrote: Dear Justin I used LigParGen server to generate ligand topology but I dont know what changes I have to do in .itp file. when I issued this command: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor faced this error:ERROR 1 [file

Re: [gmx-users] energy minimization

Dear Justin I used LigParGen server to generate ligand topology but I dont know what changes I have to do in .itp file. when I issued this command: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor faced this error:ERROR 1 [file LIG.itp, line 11]:   Atomtype opls_800 not found I

Re: [gmx-users] energy minimization

On 7/16/18 3:49 AM, farial tavakoli wrote: Dear Justin Thank you for your reply I noticed my problem ( the reason was topolgen.pl name in my directory, it is named topologen_1.1.pl in the working directory) I generated my ligand topology but got this : No output type specified. Using

Re: [gmx-users] energy minimization

Dear Justin Thank you for your reply I noticed my problem ( the reason was topolgen.pl name in my directory, it is named topologen_1.1.pl in the working directory) I generated my ligand topology but got this : No output type specified. Using default type of .top Unknown atom type: N 13 with 2

Re: [gmx-users] energy minimization

On 7/15/18 1:38 AM, farial tavakoli wrote: Dear Justin But I copied & pasted topolgen and perl5 folders in the working directory. and faced the mentioned error. Can't open perl script "topolgen.pl": No such file or directory I dont know how I should figure out this problem. The problem

Re: [gmx-users] energy minimization

Dear Justin But I copied & pasted topolgen and perl5 folders in the working directory. and faced the mentioned error. Can't open perl script "topolgen.pl": No such file or directory I dont know how I should figure out this problem. Which one of all-atom force fields will you choose to run a

Re: [gmx-users] energy minimization

On 7/14/18 5:03 AM, farial tavakoli wrote: Dear justin I am trying to run a simulation on my complex which has small molecule as a ligand , using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then installed perl script on linux. then typed "perl -v" to check if it is installed. the

Re: [gmx-users] Energy minimization of solvated MOFs.

Have you visualised the system to see what it is about that water that is generating such a high force? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu

[gmx-users] Energy minimization of solvated MOFs.

Hi I am trying to run some simulations on Metal-Organic frameworks like ZIF-8. I have obtained both structure file (from CCDC) and forcefield data from literature and I was able to successfully run energy minimization, and equilibirum MD (NVT and NPT) simulations on the crystal structure of

[gmx-users] Energy minimization with Walls

Hello, I am trying to put together a mdp script for energy minimization using 2 walls in the z direction. I have a slab of just water which is simulated fine if i remove the walls section from the script. when I add the wall section, I start to receive this error "Fatal error: DD cell 4 4 0 could

Re: [gmx-users] energy minimization

Dear Justin In according to obtaining positive binding free energy using g_mmpbsa for my complex which has 2 phosphotyrosine residues and is simulated by charmm36 force field , I sent an email to g_mmpbsa mailing list and informed them to help me for solving my problem, but they replied me : "

Re: [gmx-users] energy minimization

On 2/20/18 12:52 PM, farial tavakoli wrote: blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear Justin Thank you for the reply You meant , to tweak the emtol doesn't have

Re: [gmx-users] energy minimization

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear Justin Thank you for the reply You meant , to tweak the emtol doesn't have noticable affects on the conformational

Re: [gmx-users] energy minimization

On 2/20/18 4:52 AM, farial tavakoli wrote: Dear GMX users I used CHARMM36 all atom force field to generate .top and .gro files for my complex composed of a receptor protein and a ligand with 2 phosphotyrosine residues, then ran a md simulation on it and then used g_mmpbsa to calculate the

[gmx-users] energy minimization

Dear GMX users I used CHARMM36 all atom force field to generate .top and .gro files for my complex composed of a receptor protein and a ligand with 2 phosphotyrosine residues, then ran a md simulation on it and then used g_mmpbsa to calculate the binding free energy by pdies ( 2 and 4) but got

Re: [gmx-users] energy minimization

On Tue, Jan 9, 2018 at 4:31 PM, Justin Lemkul wrote: > > > On 1/6/18 10:10 AM, rose rahmani wrote: > >> Hi, >> >> I want to calculate the number of density profile of water.the initial >> .gro >> file which i have,has amino acid in itself, which should not be present in >> this

Re: [gmx-users] energy minimization

On 1/6/18 10:10 AM, rose rahmani wrote: Hi, I want to calculate the number of density profile of water.the initial .gro file which i have,has amino acid in itself, which should not be present in this analyze. So, i had to remove amino acid, and then, when i wanted to do energy minimization

[gmx-users] energy minimization

Hi, I want to calculate the number of density profile of water.the initial .gro file which i have,has amino acid in itself, which should not be present in this analyze. So, i had to remove amino acid, and then, when i wanted to do energy minimization again, it's crushed and gave me step files.

Re: [gmx-users] Energy Minimization Error

Dear Gromacs users, When I tried to run the equilibration run, it gave several LINCS WARNINGS. However, that equilibration run is completed by the Gromacs. Do I have to concern about these warnings or can I ignore those? Thank you. Sincerely, A. Guruge On Fri, Oct 20, 2017 at 11:22 AM, Justin

Re: [gmx-users] Energy Minimization Error

On 10/19/17 8:21 PM, Amali Guruge wrote: Dear Gromacs users, Thank you very much for the reply. My concern is "step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate". What should I do to avoid it? That happens often during

Re: [gmx-users] Energy Minimization Error

Dear Gromacs users, Thank you very much for the reply. My concern is "step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate". What should I do to avoid it? Thank you. On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul

Re: [gmx-users] Energy Minimization Error

On 10/19/17 8:10 PM, Amali Guruge wrote: Dear Gromacs Users, I tried to energy minimize my system using the steep integrator. However, it gave the following message. Steepest Descents: Tolerance (Fmax) = 5.0e+02 Number of steps= 2000 Step=0, Dmax= 1.0e-02 nm,

[gmx-users] Energy Minimization Error

Dear Gromacs Users, I tried to energy minimize my system using the steep integrator. However, it gave the following message. Steepest Descents: Tolerance (Fmax) = 5.0e+02 Number of steps= 2000 Step=0, Dmax= 1.0e-02 nm, Epot= 3.96157e+06 Fmax= 1.00697e+06, atom=

Re: [gmx-users] Energy minimization issue

On 10/16/17 5:19 AM, Khadija Amine wrote: Dear Gromacs users, I'm simulation a double chain protein-ligand complex using Amber force field. I have written parameters and generated the topology. The energy minimization of the complex gives me the following error: *Energy minimization has

[gmx-users] Energy minimization issue

Dear Gromacs users, I'm simulation a double chain protein-ligand complex using Amber force field. I have written parameters and generated the topology. The energy minimization of the complex gives me the following error: *Energy minimization has stopped, but the forces have not converged to

Re: [gmx-users] ENERGY MINIMIZATION

Hi, In a cygwin terminal, having source'd GMXRC (see the install guide), just like you need to do under Linux. Mark On Tue, Jan 10, 2017 at 7:29 PM Subashini .K wrote: > Hi Gromacs users, > > > I have installed gromacs in windows 7, 64 bit using cgywin. > > > I want to

[gmx-users] ENERGY MINIMIZATION

Hi Gromacs users, I have installed gromacs in windows 7, 64 bit using cgywin. I want to use the em.mdp file to grompp and generate a .tpr file. In which terminal should the following commands be executed? ; to test ; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v ; mdrun -v

Re: [gmx-users] Energy minimization steps

Thank you Alex and Mark for your replies. :-) Azeem > Hi, > > How many steps does it take you to walk down a mountain to a certain > village? :-) Depends where you are on the mountain, and what's in the way. > But if all you need is to be somewhere near the valley floor to start > equilibration,

Re: [gmx-users] Energy minimization steps

Hi, How many steps does it take you to walk down a mountain to a certain village? :-) Depends where you are on the mountain, and what's in the way. But if all you need is to be somewhere near the valley floor to start equilibration, anything goes! Mark On Wed, 21 Dec 2016 17:11 Alex

Re: [gmx-users] Energy minimization steps

This isn't a Gromacs-specific parameter, or, for that matter, anything that straightforwardly depends on the nature of the system (solid/fluid/protein/lipid, etc) and its size, aside from maybe trivial cases. The max number of minimization steps is something that limits an energy minimization

[gmx-users] Energy minimization steps

Hi all, What is the basis of inputting the maximum number of energy minimization steps in GROMACS? Does maximum number of energy minimization steps depend on the number of residues? I came across many articles wherein the authors have described the number of energy minimization steps within

Re: [gmx-users] Energy Minimization

solute-solvent and solvent-solvent interactions, of which you have none in the gas phase. -Justin Mishelle Sent from my Samsung device Original message From: Justin Lemkul <jalem...@vt.edu> Date: 11/03/2016 08:43 (GMT-05:00) To: gmx-us...@gromacs.org Subject: Re: [gmx

Re: [gmx-users] Energy Minimization

Positive values of potential energy and I am in vacuo. Mishelle Sent from my Samsung device Original message From: Justin Lemkul <jalem...@vt.edu> Date: 11/03/2016 08:43 (GMT-05:00) To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Energy Minimization On 11/2/16 9

Re: [gmx-users] Energy Minimization

On 11/2/16 9:40 PM, Mishelle Oña wrote: Hello I have a question about energy minimization tool. I am modelling a polymer and I use a force field I have developed. I have run a EM and got positive values. Can you help me with this? Positive values for what? Are you in vacuo or in

[gmx-users] Energy Minimization

Hello I have a question about energy minimization tool. I am modelling a polymer and I use a force field I have developed. I have run a EM and got positive values. Can you help me with this? Best regards, Mishelle -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] energy minimization

Hi Surya, I'm not sure I understand what you want to do. Do you want to energy minimise an entire trajectory? After the production phase? Why? The -c flag in mdrun is the output, the last conformation sampled during the mdrun. You can use this output file as the input structure for an energy

[gmx-users] energy minimization

Dear gromacs users, I have done simulations for 100ns. I would like to do energy minimization by using trajectory file which I got after production phase. Can I do energy minimization passing the trajectory file to -c argument? If it is yes, then tell me how to do it. Thanks in advance Surya

[gmx-users] Energy minimization, of peptide-ligand, tearing peptide apart

Hi everyone I am currently trying to perform a peptide-ligand (~4000 and 110 Da respectively) simulated annealing study using gromacs (5.1.2) with Amber force fields. Under the initial energy minimization step (minim.mdp and nvt.mdp) I am finding that the step fails. It then kicks out pdb

Re: [gmx-users] Energy minimization has stopped

Thanks a lot Justinn and Mark for the valuable suggestions. I will start over again by choosing a force field which is suitable for the RNA molecules. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun

Re: [gmx-users] Energy minimization has stopped

On 6/23/16 7:17 AM, Anurag Dobhal wrote: Dear Justin, The main aim of the study is to study the interaction between a polymer (chitosan) and RNA molecules by simulating them togather. I have already successfully simulated my polymer system using OPLS AA force field. To simulate them together

Re: [gmx-users] Energy minimization has stopped

Hi, You were recommended to pick a force field, not to combine parts of force fields. Choosing to simulate your polymer OPLS/AA if you then want to combine with RNA is not a good experimental design, unless you can do the combined simulation also in OPLS/AA. I would repeat the polymer experiment

Re: [gmx-users] Energy minimization has stopped

Dear Justin, The main aim of the study is to study the interaction between a polymer (chitosan) and RNA molecules by simulating them togather. I have already successfully simulated my polymer system using OPLS AA force field. To simulate them together I need to write the OPLS AA parameters for

Re: [gmx-users] Energy minimization has stopped

On 6/23/16 7:00 AM, Anurag Dobhal wrote: I am using OPLS AA force field. parameters (charges) for the atoms are taken from the charmm27 force field. So, by using some hybridized force field, you can't successfully minimize a structure. That should tell you something. Why are you trying

Re: [gmx-users] Energy minimization has stopped

I am using OPLS AA force field. parameters (charges) for the atoms are taken from the charmm27 force field. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul

Re: [gmx-users] Energy minimization has stopped

On 6/23/16 6:44 AM, Justin Lemkul wrote: On 6/23/16 6:35 AM, Anurag Dobhal wrote: Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force field. I have written parameters using CHARMM27 force field for RNA molecules. What does this mean? Are you using OPLS-AA or

Re: [gmx-users] Energy minimization has stopped

On 6/23/16 6:35 AM, Anurag Dobhal wrote: Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force field. I have written parameters using CHARMM27 force field for RNA molecules. What does this mean? Are you using OPLS-AA or CHARMM27? Minimising the molecule by invoking

[gmx-users] Energy minimization has stopped

Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force field. I have written parameters using CHARMM27 force field for RNA molecules. Minimising the molecule by invoking mdrun gives me the follwoing error. Energy minimization has stopped, but the forces have not converged to the

Re: [gmx-users] energy minimization error

Hi, Thanks a lot for your time and patience. This time, I chose a very simple structure and then inspected the generated topology. The interesting point was that, there were some missing interactions. When I inspected them. I found that I had defined those interactions in ffbonded.itp file, but

Re: [gmx-users] energy minimization error

Hi, pdb2gmx and grompp are pretty talkative about things like missing parameters and bonds - go back and read what they had to say, and particularly what pdb2gmx thought about your specbonds. Mark On Fri, Oct 23, 2015 at 5:51 PM faride badalkhani wrote: > Hi, > >

[gmx-users] energy minimization error

Hi, I am trying to simulate a hyper-branched polymer (a dendrimer) in water. But, every time the system blows up at energy minimization step. Therefore, according to what Mark had recommended I decided to start with a much smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had

Re: [gmx-users] energy minimization error

Hi, Did you inspect your topology like I suggested? You need to know that there are bonds exactly where you intend them, before doing any calculations with them. Mark On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani wrote: > Hi, > > I am trying to simulate a

Re: [gmx-users] Energy minimization error

Hi, As you said, I started with a G1 PAMAM dendrimer, rather than a G3 one. I had optimized it at M062x/6-31G* level, before starting the MD simulations. Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it residue by residue. After that, I started simulation procedure and

Re: [gmx-users] Energy minimization error

Dear gromacs users, As I said before I faced with the minimization error, so I changed coordinates of atoms in pdb file, but the problem is the same. the only thing that changes in every run is atom number. I modified pdb for many times. Steepest Descents converged to Fmax < 1000 in 530 steps

Re: [gmx-users] Energy minimization error

Hi, What some visualization program shows about bonds doesn't mean anything - it has not parsed your topology. You have no option but to look at the .top produced and reason about what it shows, but yours is very complex. I strongly recommend starting with something simpler than a multiply

[gmx-users] Energy minimization error

Thank you for your great help on specbond.dat file. I defined it and I could go ahead until Energy minimization step. I have used this minim.mdp file ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep

Re: [gmx-users] Energy minimization error

Hi, Look at atom 380 and see why the forces might be high. Mark On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani wrote: > Thank you for your great help on specbond.dat file. I defined it and I > could go ahead until Energy minimization step. I have used this

[gmx-users] energy minimization

Hi; I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code

[gmx-users] energy minimization

Hi; I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code

[gmx-users] energy minimization

Hi; I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code

[gmx-users] energy minimization

Hi;I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code

Re: [gmx-users] Energy minimization

On 7/8/15 8:03 PM, Malihe Hasanzadeh wrote: Hi, I want to do MD simulation of protein-DNA-ligand using Gromacs 5.0.4.,when I do energy minimization, my system is converged but has positive potential energy. also this step only takes 3 second! for next step (pr), gives error: your system is not

[gmx-users] Energy minimization

Hi, I want to do MD simulation of protein-DNA-ligand using Gromacs 5.0.4.,when I do energy minimization, my system is converged but has positive potential energy. also this step only takes 3 second! for next step (pr), gives error: your system is not equilibrated well and blowing up! I chcked my

Re: [gmx-users] energy minimization error

Hi Justin For now I used *mdrun -nt 1* * and got rid of this error so hopefully the simulation wont crash. * *Cheers* *James* On Sat, Jun 27, 2015 at 11:19 AM, James Lord jjamesgreen...@gmail.com wrote: Hi Justin, I have asked this before, but this time I started up from scratch and

Re: [gmx-users] energy minimization error

On 6/27/15 2:29 AM, James Lord wrote: Hi Justin For now I used *mdrun -nt 1* * and got rid of this error so hopefully the simulation wont crash. * The DD errors have nothing to do with physical stability; you just can't necessarily parallelize any arbitrary system over any arbitrary

Re: [gmx-users] energy minimization error

On 6/26/15 7:19 PM, James Lord wrote: Hi Justin, I have asked this before, but this time I started up from scratch and used the input files that I know they are fine but again I am getting this error, Would you please tell me what is wrong in my topology files and where about in .top files the

Re: [gmx-users] energy minimization error

Hi Justin, I have asked this before, but this time I started up from scratch and used the input files that I know they are fine but again I am getting this error, Would you please tell me what is wrong in my topology files and where about in .top files the bond length are defined?

[gmx-users] energy minimization problem

Hi, I am simulating a 5X5 carbon nanotube in the presence of nucleic acids in Tip3P water. I have made this nanotube using VMD nanotube builder and made the topology using pdb2gmx. Upto the energy minimization step every thing was fine but when I proceed for energy minimization I get the carbon

[gmx-users] energy minimization problem

Hi, The mdp file has pbc= xyz in the last line. In the previous mail it was written that pbc=full. Plaese ignore it. Thanks and regards Soumadwip -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] energy minimization problem

On 6/1/15 8:06 AM, soumadwip ghosh wrote: Thanks Justin for your quick reply. What are the correct non-bonding settings for CHARMM to be used in the .mdp file? http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM I seem to have to post this information weekly... Here is

Re: [gmx-users] energy minimization problem

On 6/1/15 9:07 AM, soumadwip ghosh wrote: Hi Justin, the snapshot I uploaded in the URL is of the SSDNA-CNT system after energy minimization step not before it. I stripped off water and ions from the system for the ease of visualization. I would be grateful if you suggest me a

Re: [gmx-users] energy minimization problem

On 6/1/15 2:28 AM, soumadwip ghosh wrote: Hi, I am simulating a 5X5 carbon nanotube in the presence of nucleic acids in Tip3P water. I have made this nanotube using VMD nanotube builder and made the topology using pdb2gmx. Upto the energy minimization step every thing was fine but when I

Re: [gmx-users] energy minimization problem

Hi Justin, the snapshot I uploaded in the URL is of the SSDNA-CNT system after energy minimization step not before it. I stripped off water and ions from the system for the ease of visualization. I would be grateful if you suggest me a possible way out. Regards, Soumadwip Research

Re: [gmx-users] energy minimization problem

Thanks Justin for your quick reply. What are the correct non-bonding settings for CHARMM to be used in the .mdp file? Here is how the CNT molecule looks like prior to energy minimization. pre energy min CNT https://drive.google.com/file/d/0B7SBnQ5YXQSLX0dIOHZjT3p1Y2s/view?usp=sharing I am not

Re: [gmx-users] energy minimization problem

Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t

Re: [gmx-users] energy minimization problem

[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps

Re: [gmx-users] energy minimization problem

...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess

Re: [gmx-users] energy minimization problem

. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi

Re: [gmx-users] energy minimization problem

Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, That's pretty quick. I guess that this is on multiple cores, given the size of the system. It often helps to equilibrate on a limited number of cores, but I'm not sure that's feasible. Did you obtain the model by martinizing

Re: [gmx-users] energy minimization problem

May 2015 6:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, That's pretty quick. I guess that this is on multiple cores, given the size of the system. It often helps to equilibrate on a limited number of cores, but I'm not sure that's

Re: [gmx-users] energy minimization problem

Sent: Monday, 18 May 2015 7:04 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem Hi Tsjerk, I used the original structure generated by sabbac. My computer has 8 cores only, martini simulation looks much faster than full atomic simulation. The command I used

Re: [gmx-users] energy minimization problem

...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10

Re: [gmx-users] energy minimization error

On 5/16/15 11:35 PM, James Lord wrote: Hi Justin Thanks for this. Can you tell me which step(s) this bond length is defined What should I do (redo) to resolve this issue? The bonds are defined in the topology. The DD algorithm reads what's in the coordinate file and builds cells based

Re: [gmx-users] energy minimization error

On 5/16/15 6:27 AM, James Lord wrote: Dear gmx users, I am getting this error, Can anyone help me to get around this? Cheers James Program mdrun, VERSION 4.6.3 Source code file: /home/james/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792 Fatal error: There is no domain decomposition for 8

Re: [gmx-users] energy minimization problem

= xyz -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Friday, 15 May 2015 11:50 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5

Re: [gmx-users] energy minimization problem

-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Friday, 15 May 2015 11:50 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/14/15 9:47 PM, Ming Tang wrote: Dear Justin, I saw

Re: [gmx-users] energy minimization problem

...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Friday, 15 May 2015 11:50 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/14/15 9:47 PM, Ming Tang wrote: Dear Justin, I saw

Re: [gmx-users] energy minimization problem

] On Behalf Of Justin Lemkul Sent: Friday, 15 May 2015 2:40 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/14/15 3:12 AM, Ming Tang wrote: Dear all, I am working with a triple helix containing around 1000 amino acids per chain using martini force field

Re: [gmx-users] energy minimization problem

On 5/14/15 9:47 PM, Ming Tang wrote: Dear Justin, I saw it in the terminal. Potential Energy = -6.3682131e+05 Maximum force = 1.8876091e+02 on atom 1147 Norm of force = 3.1155257e+00 But, how can I further minimize my protein? Minimization is not your problem. Post a full

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