Re: [gmx-users] Problem in Free Energy Calculations

H Justin, I have done the simulation of ligand in water. How ever while analyzing I found that the ligand comes out of the solvent box at the end of the simulation and during simulation too, it vibrates a lot. Please find my final md.mdp file and suggest me where am I doing wrong. ; Run

[gmx-users] umbrella sampling error

Dear all, im running umbrella sampling when invoke the following command i got the follwoing warnings and grompp terminated becasue of so much warning ,initially i neutralised the My protein-Ligand system with NACl,so how come there will be a charge? (NOTE 5)what i can do for that? can i use

Re: [gmx-users] fix simulation box corners NVE

The system is still periodic, so particles can indeed cross the boundaries. This is a good thing in the majority of cases, because the alternative, where particles are trapped, gives rise to really severe boundary effects. Kind regards, Erik > On 4 Jan 2016, at 22:15, Sereda, Yuriy

Re: [gmx-users] Force-switch algorithm

Hi, Sorry, you're right. I was thinking of the way you can have have different tables for different energy groups. But you can't have some groups using tables and some not. Mark On Tue, Jan 5, 2016 at 8:57 AM Pallavi Banerjee < pallavis...@students.iiserpune.ac.in> wrote: > Hi Mark, > > I did

Re: [gmx-users] Problem in Free Energy Calculations

Hi, On Tue, Jan 5, 2016 at 9:15 AM shagun krishna wrote: > H Justin, > > I have done the simulation of ligand in water. How ever while analyzing I > found that the ligand comes out of the solvent box at the end of the > simulation and during simulation too, it

Re: [gmx-users] Simulation of nonaqueous solvents

Okay, I will try to broadly explain what i want to do and what i need. As mentioned earlier, it would be amazing if you could direct me to some sources with these methods. I am more than 100% sure there are many liek me who will benefit from such a technique. What I want to do is study ion-pair

Re: [gmx-users] pbc

On 1/5/16 11:58 AM, Parvez Mh wrote: Dear all: I am using pbc in all directions, it is expected that, i will observe broken molecules in central box. But i am wondering, some molecules are out of box when i visualize with vmd. What would the right explanation of this? PBC is the

[gmx-users] pbc

Dear all: I am using pbc in all directions, it is expected that, i will observe broken molecules in central box. But i am wondering, some molecules are out of box when i visualize with vmd. What would the right explanation of this? Regards Masrul -- Gromacs Users mailing list * Please search

Re: [gmx-users] Simulation of nonaqueous solvents

Sorry forgot to mention, I am totally new to gromacs, so i might not be correct with some of the semantics. On Tue, Jan 5, 2016 at 3:09 PM, abhishek khetan wrote: > Okay, I will try to broadly explain what i want to do and what i need. As > mentioned earlier, it would be

Re: [gmx-users] Force-switch algorithm

Hi, On Tue, Jan 5, 2016 at 7:26 AM Mark Abraham wrote: > Hi, > > On Tue, Jan 5, 2016 at 4:46 AM Justin Lemkul wrote: > >> >> >> On 1/4/16 10:41 PM, Pallavi Banerjee wrote: >> > Hi Mark, >> > >> > Thank you for your reply. >> > >> > I want to implement

Re: [gmx-users] How to adjust the box size to correct density?

To rescale the box.gro to a desired size using the actual density 543.21 kg/l of the solvent and get a new scaled.gro file, I use this command: $ gmx editconf -f box.gro -density 543.21 -o scaled.gro > logfile On Tue, Jan 5, 2016 at 7:05 PM, Chang Woon Jang wrote: >

Re: [gmx-users] How to adjust the box size to correct density?

Dear Abhishek Khetan, Thank you for your answer. It means that Gromacs does not automatically adjust the box size even though NPT ensemble is employed. Am I right? Different from Gromacs, Lammps automatically adjust box size when NPT ensemble is applied during the simulation. Therefore, the

[gmx-users] How to adjust the box size to correct density?

Dear Gromacs Users, I have a low density polymer system initially. I would like to fit the correct liquid density using NPT simulation. I used Pcoupl=berendsen for 22 ns but the box size in confout.gro is still the same as the input size of conf.gro. Initial in conf.gro (10.0 10.0 9.8) output

Re: [gmx-users] Simulation of nonaqueous solvents

Hi, Probably it will be difficult to find the parameters for all the molecules that you want to simulate in any given FF and you are right that you should be consistent and use parameters derived in the scope of the same FF. Deriving parameters is indeed a difficult task and as far as I know good

Re: [gmx-users] How to adjust the box size to correct density?

Dear Justin, I am curious about resizing the box. My system contains 15000 atoms representing liquid polymer with very low density (maybe gas phase due to very low density). Does this very low density affect the simulation not to converge the box? Or, do the initial conditions

Re: [gmx-users] How to adjust the box size to correct density?

On 1/5/16 1:42 PM, Chang Woon Jang wrote: Dear Abhishek Khetan, Thank you for your answer. It means that Gromacs does not automatically adjust the box size even though NPT ensemble is employed. Am I right? This is incorrect. The box size will change under the influence of pressure.

Re: [gmx-users] How to adjust the box size to correct density?

On 1/5/16 2:25 PM, Chang Woon Jang wrote: Dear Justin, I am curious about resizing the box. My system contains 15000 atoms representing liquid polymer with very low density (maybe gas phase due to very low density). Does this very low density affect the simulation not to converge the box?

[gmx-users] how to adjust the box size to correct density?

Dear Gromacs Users, I have a low density polymer system initially. I would like to fit the correct liquid density using NPT simulation. I used Pcoupl=berendsen for 22 ns but the box size in confout.gro is still the same as the input size of conf.gro. Initial in conf.gro (10.0 10.0 9.8) output

Re: [gmx-users] Simulation of nonaqueous solvents

On 1/5/16 1:30 PM, Diana Lousa wrote: Hi, Probably it will be difficult to find the parameters for all the molecules that you want to simulate in any given FF and you are right that you should be consistent and use parameters derived in the scope of the same FF. Deriving parameters is indeed a

Re: [gmx-users] Simulation of nonaqueous solvents

i checked out all the suggestions 1) the oplsaa topology and forcefields are available in for all the solvents that i wanted from http://virtualchemistry.org . 2) The database in share/gromacs/top does contain some solvents and ions too but mostly for only the cations. Cl- was the lone anion. 3)

Re: [gmx-users] how to adjust the box size to correct density?

Hi, On Tue, Jan 5, 2016 at 7:15 PM Chang Woon Jang wrote: > Dear Gromacs Users, > > > I have a low density polymer system initially. I would like to fit the > correct liquid density using NPT simulation. > > I used Pcoupl=berendsen for 22 ns but the box size in

Re: [gmx-users] how to adjust the box size to correct density?

Hi, Look at what md.log says about the value for pcoupl it read from your .tpr. :-) Mark On Tue, Jan 5, 2016 at 9:39 PM Chang Woon Jang wrote: > Dear Mark, > > I obtained the tpr file with gro and topology file using grompp -v. > > The following is from md.log file. >

Re: [gmx-users] how to adjust the box size to correct density?

Dear Mark, I see. pcoupl = No is obvious. That means when I create tpr file from grompp.mdp, the pcoupl setting was No instead of berendsen. Thank you very much. Best regards, Changwoon Jang On Tue, Jan 5, 2016 at 3:41 PM, Mark Abraham wrote: > Hi, > > Look at

Re: [gmx-users] How to adjust the box size to correct density?

Dear Justin, Please take a look at the file. I modified mdp file provided from VOTCA tutorial. I think that mdp file is ok. Thank you very much. Best regards, Changwoon Jang On Tue, Jan 5, 2016 at 2:45 PM, Chang Woon Jang wrote: > Dear Justin, > > Please take a

Re: [gmx-users] How to adjust the box size to correct density?

Dear Justin, The following is from .mdf file. ; VARIOUS PREPROCESSING OPTIONS include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps

Re: [gmx-users] Force-switch algorithm

Hi Mark, Thanks a lot! All the discussions were of great help. -Pallavi Banerjee -- 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 http://www.gromacs.org/Support/Mailing_Lists * For

[gmx-users] Regarding value of Elj, Eqq, Clj and Cqq values using LIE Approach

Dear Gmx-user, I am using LIE approach to calculate the binding energy of my protein and ligand. When I am running g_lie program for my protein I am getting the value of DeltaG= 0. Can you please suggest me a way to get the values of Elj, Eqq, Clj and Cqq and also about the post-processing

[gmx-users] pmf-gwham

Dear All, I am doing umbrella sample for a system and I have a question. on my system I have extra two angle_restraints_z on the pulled group, and one position restrain on the reference group. Dose g-wham accept having this number of restrains on the system. Dose having many restrains

[gmx-users] Constraints in BAR

Hello everyone, I've got a question about the current implementation of BAR and constraints. Is the issue discussed in the following thread still a problem in current versions of gromacs? https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2010-October/004841.html Thanks in

Re: [gmx-users] Simulation of nonaqueous solvents

Hi, I am not completely sure of what you intend to do, i.e. do you want to simulate just the ions in solution or do you want to study protein-ion interactions in nonaqueous solvents? The latter issue has been addressed by us in this work http://pubs.acs.org/doi/abs/10.1021/jp303008g. You can find

Re: [gmx-users] Protein-Protein distance

I am little confued to use the gmx distance command specifically for my purpose mentioned in my question ; gmx distance -f file.xtc -s file.gro -n file.ndx for outputting the distance between protein 1 and protein 2, protein 1 and protein 3 , protein 1 and protein 4 I will use -oav or -oxyz or

Re: [gmx-users] Protein-Protein distance

OK , Thanks a lot now I got it , if I feel any difficulty further I will ask. Thank you On Wed, Jan 6, 2016 at 2:42 AM, Justin Lemkul wrote: > > > On 1/5/16 4:11 PM, Life Sciences Inc wrote: > >> I am little confued to use the gmx distance command specifically for my >>

Re: [gmx-users] Protein-Protein distance

On 1/5/16 4:11 PM, Life Sciences Inc wrote: I am little confued to use the gmx distance command specifically for my purpose mentioned in my question ; gmx distance -f file.xtc -s file.gro -n file.ndx for outputting the distance between protein 1 and protein 2, protein 1 and protein 3 ,

[gmx-users] There is no domain decomposition

Dear users, I get "domain decomposition error" in the energy minimization step of an apo-protein. The last part of the log file is below. log file: ... Initializing Domain Decomposition on 24 ranks Dynamic load balancing: no Will sort the charge groups at every domain (re)decomposition Initial

Re: [gmx-users] how to adjust the box size to correct density?

Dear Mark, I obtained the tpr file with gro and topology file using grompp -v. The following is from md.log file. Best regards, Changwoon Jang Log file opened on Fri Nov 13 13:52:29 2015 Host: c438-702.stampede.tacc.utexas.edu pid: 8923 rank ID: 0 number of ranks: 64 GROMACS:

Re: [gmx-users] Problem in Free Energy Calculations

On 1/5/16 1:34 AM, shagun krishna wrote: Hi Justin.. Thanks a ton to you. Finally I have completed the simulation of ligand in solvent. In your earlier mail you have written that to calculate the binding energy of protein-ligand I will need the nonbonded interaction energy between

Re: [gmx-users] umbrella sampling error

On 1/5/16 5:36 AM, Nikhil Maroli wrote: Dear all, im running umbrella sampling when invoke the following command i got the follwoing warnings and grompp terminated becasue of so much warning ,initially i neutralised the My protein-Ligand system with NACl,so how come there will be a charge?

Re: [gmx-users] draw histogram

On 1/5/16 1:01 AM, Sana Saeed wrote: hi gmx usersi am trying to plot histogram.xvg , but the graph isn't making any sense, or may be i dont understand it.in the gromacs tutorial from bevanlab (free energy calculations:methane) it says that we need to separate the data. how? You'll need

Re: [gmx-users] Protein-Protein distance

On 1/5/16 1:18 AM, Life Sciences Inc wrote: Dear Gromacs Users Kindly let me know how to calculate the protein protein distance as a function of time with gromacs. I want to calculate the distance based on the center of mass of the selection which is CA atoms. I have 4 proteins in the system

Re: [gmx-users] US perl scripts fails index error

On 1/5/16 4:06 AM, Nikhil wrote: Thank you very much Justin, i fixed it,i run the script when i analyzing the summary_distance.dat i seen some filed is left blank,as below 389 3.989 390 4.029 391 4.014 392 393 4.103 394 4.147 395 396 4.188 397 398