Re: [gmx-users] PEG from ATB: No residues in chain

Hi, Why do you need to execute gmx pdb2gmx if you already retrieved parameters from ATB? ATB should be able to provide you the coordinate and topology files (.gro and .itp respectively) compatible with GROMACS. Soumadwip -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] contact analysis between the all backbone of same protein

. It will ask you for the group only once. Then post process the .xpm file into an eps file using, gmx xpm2ps -f dm.xpm -o dm.eps -rainbow red One can view the .eps file in eps viewer and convert it into a .png or .tiff file. Best of luck! Soumadwip Ghosh Post Doctoral Research Associate Dept

Re: [gmx-users] gro to itp file

Hi, You said you ran pdb2gmx to convert pdb to gro. This should also give you the topology if you typed something like gmx pdb2gmx -f lig.pdb -o lig.gro It should give you lig.itp, topol.top and a posre.itp since u have already updated the .rtp file. Hope this helps Soumadwip -- Gromacs

Re: [gmx-users] Extending MD simulations

Hi Akash, The correct command would be: gmx mdrun -s new.tpr -v -deffnm md_0_1 -cpi md_0_1.cpt ( -append option is optional) . This should start appending your files from the previous 60 ns simulation. Best, Soumadwip Ghosh -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] Structures after Dihedral principle component analysis (dPCA)

combined .xvg file to find out what is the corresponding time stamp of that. Once you get this, it should not be a problem dumping out that particular snapshot using gmx trjconv. Best, Soumadwip Ghosh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] Structures after Dihedral principle component analysis (dPCA)

Hi, It seems that you have got PC1, PC2 and Gibb's free energy in the x, y and z axes respectively. If I am not wrong you first combined the pc1.xvg and pc2.xvg to a single .xvg file compatible with gmx sham. Right? Then, You must have converted the .xpm output from gmx sham to a text file and

[gmx-users] g_mindsit contact analysis

then the total contacts will be 3000. Is it being calculated this way or something else is going on? Thank you for your answer in advance Soumadwip Ghosh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] Fwd: lost particles while sorting

2in/view?usp=sharing https://drive.google.com/file/d/1iFskowIggdFkNlJwkQJ_LbeumV- QtUZ2/view?usp=sharing Regards, Soumadwip Ghosh -- 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 h

[gmx-users] lost particles while sorting

usp=sharing Regards, Soumadwip Ghosh -- 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 (un)subscribe requests visit ht

Re: [gmx-users] Regarding calculating the water orientation profile

to the N terminus or vice versa. Let me know if you get it done. Best of luck! Soumadwip Ghosh Post Doctoral Research Associate City of Hope National Medical Center Duarte, CA 91010 United States -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] Protein almost detaching from the micellar core

Mark Sansom's eminent research group. I will be obliged if someone guides me a little bit in this regard. Any literature or material which include such observation will be really helpful in understanding whats going on. Thanks in advance Soumadwip Ghosh Post Doctoral Research Associate Prof

[gmx-users] Clustering based on other parameters than RMSD

? I would appreciate any input on this regard. Thanks and regards, Soumadwip Ghosh Post Doctoral Research Associate Prof. Vaidehi Nagarajan's group Department of Molecular Immunology City of Hope Cancer Research Center Duarte, CA 91010 United States -- Gromacs Users mailing list * Please search

[gmx-users] Clustering based on other parameters than RMSD

Hi all, I have a trajectory of 300 ns for a membrane protein. I want to sample native/non-native conformations and compare across various systems. My question is can parameters like number/occupancy of hbonds or the time evolution of helical residues (output from gmx do_dssp) be clusterized using

Re: [gmx-users] Coordinates not matching with topology file

you don't mix and match between the two. Best of luck Soumadwip Ghosh Post Doctoral Research Fellow City of Hope Cancer Research Center Duarte 91010, CA USA -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

Re: [gmx-users] Ionic liquid simulation problem

else. Best Soumadwip Ghosh Post Doctoral Research Associate City of Hope Cancer Research Center Duarte 91010 CA USA -- 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

[gmx-users] Installing DSSP

command we get the following error : Fatal error: DSSP executable (usr/local/bin/dssp/dssp) does not exist (use setenv DSSP) PS. we are using bash I have read various threads on the errors related to do_dssp but could not find a solution. Any kind of help would be appreciated. Best, Soumadwip

[gmx-users] gmx insert-molecules not adding the required number of molecules

with OPLS-AA force field. Thnaks and regards, Soumadwip Ghosh Research Associate Indian Institute of Technology Bombay India -- 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

[gmx-users] Capping the termini of a protein

of the configuration file? Thanks for your help in advance. Soumadwip Ghosh IITB, Mumbai India -- 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

[gmx-users] Fwd: protein getting unfolded in SPC/E water

-- Forwarded message -- From: soumadwip ghosh <soumadwipgh...@gmail.com> Date: Thu, Sep 15, 2016 at 9:16 PM Subject: protein getting unfolded in SPC/E water To: "gromacs.org_gmx-users" <gromacs.org_gmx-users@maillist.sys.kth.se> Hello, I am simul

[gmx-users] protein getting unfolded in SPC/E water

0.0063 0.835859 0.0314951 (nm^3) Density 1012.78 0.0182.41171 -0.0908186 (kg/m^3) What might go wrong? Thanks for your time in advance. Soumadwip Ghosh Senior Research Fellow Indian Institute of Technology Bombay India -- Gromacs Users mailing list * Pleas

[gmx-users] Sigma and epsilon parameters for water and graphene atoms

and then calculate the combinations (such as sigma CO and epsilon CO). Am I guessing it right? Any kind of help will be appreciated. Thanks and Regards, Soumadwip Ghosh Senior Research Fellow IITB Mumbai India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

[gmx-users] Topology of a neutral single peptide

excuse me if I am asking for much. Thanks in advance for your time. Soumadwip Ghosh Senior Research Scholar IIT Bombay India -- 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

[gmx-users] Simulation getting slower and ultimately crashing

05:16:18 2016 I am guessing there are some issues with the PME calculations and the number of nodes used for a smaller system like mine. In that case what would be the correct combination for options such as -npme or -nt? Should I use the -dlb option? I would love to hear from the experts. Thanks i

[gmx-users] Fwd: Simulation getting slower and ultimately crashing

-- Forwarded message -- From: soumadwip ghosh <soumadwipgh...@gmail.com> Date: Wed, Apr 27, 2016 at 2:52 PM Subject: Simulation getting slower and ultimately crashing To: "gromacs.org_gmx-users" <gromacs.org_gmx-users@maillist.sys.kth.se> Hi, I am sim

Re: [gmx-users] Simulation getting slower and ultimately crashing

what would be the correct combination for options such as -npme or -nt? Should I use the -dlb option? I would love to hear fro the experts. Soumadwip Ghosh Senior Research Fellow IITB India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing

[gmx-users] Simulation getting slower and ultimately crashing

om/open?id=0B7SBnQ5YXQSLZ0k3QnJPaXBmbnc the hybrid.pdb file (containing the NA+CNT): https://drive.google.com/open?id=0B7SBnQ5YXQSLTEpibVByTEg4N0E the md.mdp file: https://drive.google.com/open?id=0B7SBnQ5YXQSLMmd1di1jbHpubFE Thanks in advance Soumadwip Ghosh Senior Research Scholar IITB India -- Gromacs Use

Re: [gmx-users] Graphene sheet topology

my fingers crossed. 3. I am keeping the dihedral function type 1 as per your suggestion. Please let me know if what I am doing right now as mentioned above makes sense or not. I will update on the outcomes of my simulation even if everything goes right. Thanks once again for the reply Justin..:)

Re: [gmx-users] Graphene sheet topology

tps://drive.google.com/open?id=0B7SBnQ5YXQSLdXZDZVNDOFJqVDg PS: I forgot to issue the -pbc while executing the g_x2top command and also did not change the dihedral function type from 1 to 3 as suggested in the tutorial. Can this be a reason for the above error to occur? Thanks and regards, Soumadwip Ghosh Sen

[gmx-users] Graphene sheet topology

sue the -pbc while executing the g_x2top command and also did not change the dihedral function type from 1 to 3 as suggested in the tutorial. Can this be a reason for the above error to occur? Thanks and regards, Soumadwip Ghosh Senior Research Scholar Indian Institute of Technology Bombay In

Re: [gmx-users] sigma and epsilon values for C and H atoms in CNT

Hi, the atomtype descriptions for CNT in CHARMM27 force field are CA and HP for carbon and hydrogen respectively( both of them aromatic). You will find the sigma and epsilon values in the ffnonbonded.itp of the CHARMM27 ff directory. Best of luck. Soumadwip -- Gromacs Users mailing list *

[gmx-users] CNT using g_x2top

://drive.google.com/file/d/0B7SBnQ5YXQSLWjFab1NIMmFiQVk/view?usp=sharing for the cnt.itp file and https://drive.google.com/file/d/0B7SBnQ5YXQSLd3gtRFFrTTA4Wlk/view?usp=sharing for the minim.mdp file. Any kind of help will be hugely appreciated. Regards, Soumadwip Ghosh Senior Research Fellow IITB India

[gmx-users] dna topology in OPLS force field

in this regard. Sorry for asking much. Thanks and regards, Soumadwip Ghosh Senior Research Fellow IIT Bombay India -- 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

Re: [gmx-users] Query about g_mindist

in some literature or in GROMCS documentation somewhere) which governs this time evolution? I did not find one. I would appreciate your thoughts on this. As you can see I am trying to probe how the RNA and CNT are interacting with each other on a primary level. Regards, Soumadwip Ghosh Research

[gmx-users] Query about g_mindist

, Soumadwip Ghosh Senior Research Scholar IITB India -- 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 (un)subscribe requests visit https

[gmx-users] How to calculate which residues are within a certain distance from a carbon nanotube

not residue as a function of time. Can g_mindist in combination with -d 0.5 and -respertime serve the above purpose? Or should I try with g_select? Sorry if I am asking for much. Thanks and regards, Soumadwip Ghosh Research Fellow IITB Mumbai India -- Gromacs Users mailing list * Please search

[gmx-users] radial density profile

method? Many thanks in advance. Soumadwip Ghosh Research Fellow IITB Mumbai India -- 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 (un

Re: [gmx-users] using OH ions in combination with CHARMM27 force field

Thanks Justin for your help. I will carry out the simulation with 0.1M NaOH which I had previously (the coordinate and the topology) and let you know if the desired interactions are taking place or not. Cheers, Soumadwip -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] using OH ions in combination with CHARMM27 force field

on this. I would also like to know if I make an NaOH.itp somehow and then add it to my system containing the polymer is it going to behave like a polyelectrolyte? Sorry if I am asking much. Thanks and regards, Soumadwip Ghosh Research Scholar IITB India -- Gromacs Users mailing list * Please search

[gmx-users] using OH ions in combination with CHARMM27 force field

[ system ] nafion and ions in water [ molecules ] LIG 1 SOL7997 NA 15 OH 15 Regards, Soumadwip Ghosh Research Scholar IITB India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-U

Re: [gmx-users] Gromacs

Hi, How is it possible that you have finished up to production run without the .top file ? The first line of your ebolaag.top says that the topology has been generated. How have you been doing any of the equilibration steps without the .top file? Information regarding atoms are there in the

Re: [gmx-users] No domain decomposition

Hi Chandan, I tried it once using -nt option but it failed . I kept it 8 although I dont know how to change the number of nodes for mdrun correctly. How do I know the value of x if I want to run say mdun -deffnm mdfinal -nt x. It is worth mentioning here that for my NPT and NVT

Re: [gmx-users] no domain decomposition

converged or the problem is something else? Any kind of help would be appreciated. Thanks and regards, Soumadwip Ghosh Research Fellow, IITB Mumbai India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

Re: [gmx-users] swissparm .itp problems

Hi, You should cut+paste the [ atomtypes ] and the [ pairtypes ] in a new atomtypes_ligand.itp file so that your ligand.itp starts from the directive [ moleculetype ]. Now, add the atomtypes_ligand.itp in your topology file before the ; Include chain topologies part. Hope this helps Cheers,

[gmx-users] No domain decomposition

Hi all, I am simulating a swCNT-ssDNA hybrid ( dna encapsulated in CNT) in the presence of some organic fillers. I made the topologies using pdb2gmx and until the energy minimization mdrun step everything was fine. I used the following command to for energy minimization mdrun -deffnm em --

Re: [gmx-users] No domain decomposition

ent coordinates Wrote pdb files with previous and current coordinates Segmentation fault (core dumped) What should I do? Was the command used for mdrun ( -nt 8) wrong? Am I missing something important. Your help will be appreciated. Thanks and regards, Soumadwip Ghosh Research Fellow IITB Mumbai In

[gmx-users] No domain decomposition

pid. I tried playing around with options such as -nt, -npme and all but this error is still popping up. Thanks for your time in advance. Soumadwip Ghosh Research Fellow IITB Mumbai India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/

Re: [gmx-users] No domain decomposition

s of now I can't see a way out apart from setting up the system again. But I am 100% sure that there was nothing wrong with the topologies. Thanks and regards, Soumadwip Ghosh Research Fellow IITB Mumbai India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.o

Re: [gmx-users] no domain decomposition

Hi Mark and Justin, actually I have simulated each item with pure SPCE water separately for a few nanoseconds and they are absolutely fine. The initial structure ( a small dna inside a CNT) was generated using Packmol and may be due to this I have this error occuring each time. Justin

[gmx-users] initial structure generation for performing MD simulations

). Can anyone suggest me a way to build up my initial structure or do I have to run a short simulation to achieve the same (ref. Gao et al. 2006. Nano Letters)? Thanks for your time in advance Soumadwip Ghosh Research Fellow IITB Mumbai India -- Gromacs Users mailing list * Please search

[gmx-users] calculation of persistence length

nds are given. Can anyone help resolving the issue? Thanks in advance, Soumadwip Ghosh Research Fellow, IITB Mumbai India -- 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.gro

[gmx-users] Unwrapping of ssDNA

of the said unwrapping if the salt concentration is raised from the perspective of my understanding or I am going terribly wrong somewhere? I would be grateful to any sort of discussion in this regard. Thanking you, Soumadwip Ghosh Senior Research Fellow IITB Mumbai India -- Gromacs Users mailing list

[gmx-users] Unwrapping of ssNA

of the said unwrapping if the salt concentration is raised from the prospective of my understanding or I am going terribly wrong somewhere? I would be grateful to any sort of discussion in this regard. Thanking you, Soumadwip Ghosh Senior Research Fellow IITB Mumbai India -- Gromacs Users mailing list

[gmx-users] regarding box volume

Ignore the previous mail. Hi, please excuse me if my question appears very silly to you. I have a hybrid of a Carbon nanotube and a polymer and I want to study the unwrapping dynamics of the polymer in presence of a polymer binding agent. I kept the hybrid inside a triclinic box and am doing

[gmx-users] box volume

be missing out something very fundamental. Your help would be appreciated. Sorry if I am asking for much. Soumadwip Ghosh Research Fellow IITB Mumbai India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

Re: [gmx-users] Single point energy calculations

Thanks Mark. I will do it..:-) Regards, Soumadwip -- 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 (un)subscribe requests visit

[gmx-users] Single point energy calculations

any sort of help. I have never done single point energy calculations using MD simulations and sorry for asking much. Thanks and regards, Soumadwip Ghosh Senior Research Fellow IITB India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] em_cnt_rna.jpg

I've shared an item with you: em_cnt_rna.jpg https://drive.google.com/file/d/0B7SBnQ5YXQSLX0dIOHZjT3p1Y2s/view?usp=sharinginvite=CNLmj6gE It's not an attachment -- it's stored online. To open this item, just click the link above. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] MD simulations

What is the error displayed when you run grompp? Is it related to the topology mismatch, wrong mdp parameters, domain decomposition error, shake/Lincs error or something else? There are so many possibilities and unless you write the exact error statement issued by grompp it is impossible for

[gmx-users] RDF

Is there something wrong with my approach. FYI I took 8 SDS binders which wraps around the fullerene molecule. I think I am missing out something very trivial. Any kind of help will be appreciated. Soumadwip Ghosh Research Fellow IITB India -- Gromacs Users mailing list * Please search

Re: [gmx-users] position restraining of ions

Hi, this problem usually arises when there are more than one species of a perticular kind is present in your conf.gro file. In your case you have 85 potassium and 122 chloride ions in the input .gro file you used while generating individual ion posre.itp files. However, in the ions.itp file in

[gmx-users] Deformation of DNA duplex

calculate those parameters from GROMACS? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439907/pdf/gks517.pdf How can I show the time evolution of fraction of native contacts for my DNA chain? Sorry if I am asking for much. Thanks for your time in advance. Regards, Soumadwip Ghosh Research Fellow, IITB

[gmx-users] deformation of DNA duplex

calculate those parameters from GROMACS? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439907/pdf/gks517.pdf How can I show the time evolution of fraction of native contacts for my DNA chain? Sorry if I am asking for much. Thanks for your time in advance. Regards, Soumadwip Ghosh Research Fellow, IITB

Re: [gmx-users] Problem with the MDS extended trajectory in GROMACS 5.0.4

Hi, Say your initial mdrun command for 30 ns were as follow grompp_mpi -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o md_0_1.tpr and mdrun_mpi -deffnm md_0_1 Then you should get the files such as md_0_1.xtc, md_0_1.log, md_0_1.edr, md_0_1.cpt, md_0_1.trr and so on Then you obtain a new

Re: [gmx-users] Hydrogen bonds

Hi, the -hbn option in g_hbond in connection to your issue of determining the hydrogen bond lifetime or stability does not tell you much. What you should be looking at is running the g_hbond with -ac flag which gives you the lifetime and H-bond formation energy between two groups specified by

Re: [gmx-users] Hydrogen bonds

As a said the -hbn option in g_hbond is probably not informative in your case. First tell us what do you really want to observe? The no. of hydrogen bonds between specific amino acid residues and your ligand binding sites? If yes, use g_hbond with -num option that will give you the exact no of

[gmx-users] Temperature variation of CHARMM force field

density profile it will be a valid point in connection with the comment from the reviewer? If this is the case, is it the npt.edr or the md.edr file where I should look for the density? Any opinion regarding this would be of great help. Thanks and regards, Soumadwip Ghosh Research Fellow IITB India

[gmx-users] temperature variation of all-atom CHARMM force fields

with an appropriate response to the reviewer? Sorry if I am asking for much. Thank you for your time in advance. Regards Soumadwip Ghosh Research Fellow IITB India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] temperature variation of all-atom CHARMM force field

it will be a valid point in connection with the comment from the reviewer? If this is the case, is it the npt.edr or the md.edr file where I should look for the density? Any opinion regarding this would be of great help. Thanks and regards, Soumadwip Ghosh Research Fellow IITB India -- Gromacs

Re: [gmx-users] calculation radial concentration plots

Thanks for an early reply. In the link provided I can see that CANION requires an Amber output file whereas my output files are GROMACS generated and I used CHARMM 27 force field for carrying out md simulations. Another thing is that I am a newbie in computational studies and I really dont know

[gmx-users] calculation radial concentration plots

atoms and then obtain curves like that of figure 7 using equation 2 of the above reference. Thanks for your help in advance. Soumadwip Ghosh Research Fellow IITB India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] VOlume of box

Hi, Check the md.gro file. The box lengths in each dimension are given at the end of the production run .gro file. Ideally, the box length or the volume should not change (within error bars) provided that the NPT equilibration step is carried out properly. Soumadwip -- Gromacs Users mailing

Re: [gmx-users] Error in volume coupling, no domain decomposition

Hi, Is there a possibility that your system is too small and thus the domain decomposition can't take place within the 16 processor you are using? Try to alter the number of terminals using -nt ( keep 1) option or play around with decreasing the time step or increasing the box length. Follow

[gmx-users] About g_helix

how it works? Many thanks in advance. Soumadwip Ghosh Research Fellow IITB India -- 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 (un

[gmx-users] About g_helix

how it works? Many thanks in advance. Soumadwip Ghosh Research Fellow IITB India -- 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 (un

[gmx-users] Ion binding to DNA

time in advance Soumadwip Ghosh Research Scholar IITB india -- 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 (un)subscribe requests visit

[gmx-users] regarding topology

Hi, I have a question about the topology made by SwissParam which is compatible with CHARMM 27 force field. I hate to bring the same thing up again and again but I am really doubtful about some of the parameters created by the above mentioned web server. I have built a topology for fullerene

[gmx-users] Regarding SwissParam topology

Hi, I have a question about the topology made by SwissParam which is compatible with CHARMM 27 force field. I hate to bring the same thing up again and again but I am really doubtful about some of the parameters created by the above mentioned web server. I have built a topology for fullerene

[gmx-users] Using g_spatial

asking for much. Regards, Soumadwip Ghosh Research Fellow IITB India -- 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 (un)subscribe

[gmx-users] nvt equilibration

Hi, did you specify the groups you made as energygroups in the nvt.mdp file? What do u want to achieve with these index groups? If you want to find out the non-bonding interactions among them, you must tag them as specific groups in the .mdp file before issuing grompp. Soumadwip -- Gromacs

[gmx-users] Using g_spatial

. Regards, Soumadwip Ghosh Research Fellow IITB India -- 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 (un)subscribe requests visit https

Re: [gmx-users] temperature problem

Hi, reconstruct both the .mdp (NVT, Md) files as follows- tc_groups = Protein Non-protein tau_t =0.1 0.1 ref_t =300 300 This should work. Soumadwip -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] fullerene crashes during energy minimization

Are you sure you are using the correct force field? Did you ignore any warning given by grompp before doing mdrun for energy minimization? Try altering the box size/ shape in the configuration file or and/or reduce the time step. If the problem still persists may be there is something wrong in the

[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

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] regarding pdb2gmx

Thank you very much for your help Justin. I really appreciate I would like to bother you for one last time ( as of now ;). So, if I am dealing with a non-trivial molecule like CNT or some polyelectrolyte and I mainly intend to demonstrate the non-bonding interactions with some nucleic acids (say

[gmx-users] regarding pdb2gmx

be highly obliged. Sorry if I am asking for much. Soumadwip Ghosh Research Fellow IITB India -- 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

Re: [gmx-users] regarding pdb2gmx

Thanks Justin for your insights. So when I am making the topology of DNA via ppdb2gmx using CHARMM, the parameters in the .itp files are not adequate and I should place them manually everytime I make a molecule topology with pdb2gmx? In some of my previous works actually the DNA molecule gave

[gmx-users] PDB files

Hi all, I have a general query about PDB files. I have made a PDB file for a carbon nanotube (15x15) using VMD which contains 1600 carbon atoms. As far as I know, the PDB file should contain atom no. in lines 13-16 and the residue id in line 18-20. Now,I obtained the pdb file from VMD as

[gmx-users] #include section for a .top file

Dear GMX users, I am simulating some polyelectrolytes in the presence of a large organic cation. I have made both the .itp files from SWIISPARAM web server since I am using CHARMM27 force field. Next, I made the topology file for GROMACS like this- GROMACS topology ; ;

[gmx-users] #include section in a .top file

Ignore the previous incomplete mail. Dear GMX users, I am simulating some polyelectrolytes in the presence of a large organic cation. I have made both the .itp files from SWIISPARAM web server since I am using CHARMM27 force field. Next, I made the topology file for

Re: [gmx-users] #include section in a .top file

Thanks Justin as always for your help. Actually, the atomtype CR -- 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 (un)subscribe

Re: [gmx-users] #include section in a .top file

Plaese ignore the previous mail. Thanks Justin for your help as always. Actually, the atomtype CR was common to both the building units of the polymer as well as the cation built by SWISSPARAM. I generally dont use maxwarn at all but I too thought of the warning being not harmful since the

Re: [gmx-users] Simulation of Ethanol

Hi, U haven't mentioned the error bar of the resulting density of ethanol. Moreover, what were the nvt and npt parameters? Without these it is difficult to suggest a solution.. Cheers Soumadwip -- Gromacs Users mailing list * Please search the archive at

[gmx-users] H-bonding

Hello all, I am trying to see what happens to the no. of Watson-Crick hydrogen bonds between two parallel chains of a double stranded DNA on incorporating a flat graphene sheet. The no of interchain H-bonds are supposed to decrease with time. But I am not sure how to use g_hbond in

[gmx-users] H-bond query

Hello all, I am trying to see what happens to the no. of Watson-Crick hydrogen bonds between two parallel chains of a double stranded DNA on incorporating a flat graphene sheet. The no of interchain H-bonds are supposed to decrease with time. But I am not sure how to use g_hbond in

[gmx-users] query regarding itp file

Hi all, I have some general doubts about the use of an itp file built by some software. I am studying the dynamics of a DNA in presence of a graphene sheet. I am using now the CHARMM27 force field and have obtained a graphene.itp file from PARAMCHEM where the atom types of the sp2 carbon

Re: [gmx-users] position resrtraints

Dear Justin, thanka 4 ur prompt reply. I checked that there was another issue. I didnot modify the aminoacids.rtp file in order to incorporate the new graphene.pdb atom types according to the force field. It appears to me that the correct interaction is not arsising because the

[gmx-users] position rstraints

Hi all, I am trying to see the unzipping of double stranded DNA on the surface of graphene nanosheets. I am using GROMOS 53a5 force field and I obtained a graphene sheet from ATB software. i obtained both the .itp as well as the PDB from that site. Now, I proceeded for molecular dynamics

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