Re: [gmx-users] PMF of ligand transport

Hi Chris, Thank you very much for your detailed mail. Now I have a doubt on this pull_init parameter. i read your previous posts regarding this, but still have a confusion. My query is that for each configuration when I run umbrella sampling, will this pull_init value needs to change?(I suppose

RE: [gmx-users] non zero charge in topolgy

You can call the following whatever you want to: [ moleculetype ] ; Namenrexcl Protein 3 This would probably be more appropriate: [ moleculetype ] ; Namenrexcl Hexane 3 And this section, doesn't really matter what it says here either, this par

Re: [gmx-users] Learning MD

Thanks a lot for your replies. I will start reading this and learning MD. I really want to say that this forum is an excellent source of help. Thanks for all your help. Regards -- Sonali Dhindwal --- On Mon, 10/5/10, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] Lear

[gmx-users] non zero charge in topolgy

Compound#mols Protein 1 -- next part ------ An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100510/a4bbc6df/attachment.html -- -- gmx-users mailing list gmx-users@gromacs.org ht

Re: [gmx-users] non zero charge in topolgy

Moeed wrote: Dear experts, 1- I am trying to produce tpr file for EM (there is one hexane molecule in my system). It seems top file has non zero charge. could you please help me how to deal with this problem. You have the wrong sign on the charge of C3. 2-To run the simulation for one s

[gmx-users] non zero charge in topolgy

Dear experts, 1- I am trying to produce tpr file for EM (there is one hexane molecule in my system). It seems top file has non zero charge. could you please help me how to deal with this problem. 2-To run the simulation for one single hexane molecule what should the box size be? it is- box 3 3 3

Re: [gmx-users] Re: configure error

On 11/05/2010 12:13 AM, Emily Curtis wrote: Hi Lina, I am sorry to ask you about this again but I am having trouble finding the post you mentioned: gmx-users Digest, Vol 72, Issue 18. I ran autoreconf but it didn't work. Do you have to use version 2.13 or just any version later than 2.13. I r

Re: [gmx-users] g_dist error?

Marc Charendoff wrote: Hello, I am in the middle of analyzing the distance between two atoms of a MD trajectory when I ran into the following error thus stopping at 3 ns of a 4 ns trajectory. What could be the issue? Select a group: 18 Selected 18: 'a_1899' Select a group: 19 Selecte

[gmx-users] g_dist error?

Hello, I am in the middle of analyzing the distance between two atoms of a MD trajectory when I ran into the following error thus stopping at 3 ns of a 4 ns trajectory. What could be the issue? Select a group: 18 Selected 18: 'a_1899' Select a group: 19 Selected 19: 'a_2498' trn version:

Re: [gmx-users] OPLS benzene issue

On 5/10/10 9:29 PM, Jeffery Perkins wrote: Hello Gromacs users, I've been trying to run a system of benzene at 298 K and 1 bar as a test for future use as a solvent and have built it in OPLS using opls_145 for the carbons and opls_146 for the hydrogens, these are listed in the ffoplsaa files as

[gmx-users] Re: python wrapper from libxdr?

Bin, no you are not missing something. It is not in the distribution as I though it is. You can get it with git: git clone git://git.gromacs.org/libxdrfile.git @David: How come that it is not in the distribution? Is this on purpose or error in "make dist"? Roland On Mon, May 10, 2010 at 3:06 P

[gmx-users] OPLS benzene issue

Hello Gromacs users, I've been trying to run a system of benzene at 298 K and 1 bar as a test for future use as a solvent and have built it in OPLS using opls_145 for the carbons and opls_146 for the hydrogens, these are listed in the ffoplsaa files as benzene parameters. However I've found tha

[gmx-users] Re: python wrapper from libxdr?

Dear Roland: Thanks for your reply. I checked both the distribution at the link you provided, and none of them has any python files. Am I missing something here? Best, Bin On May 10, 2010, at 11:56 AM, Roland Schulz wrote: Hi, yes this python wrapper is part of xdrfile. And can be downl

[gmx-users] Re: python wrapper from libxdr?

Hi, yes this python wrapper is part of xdrfile. And can be downloaded from the GROMACS website: http://www.gromacs.org/index.php?title=Download_%26_Installation Roland On Mon, May 10, 2010 at 1:42 PM, BIN ZHANG wrote: > Dear all: > > I found this really interesting email on the mail list about

[gmx-users] python wrapper from libxdr?

Dear all: I found this really interesting email on the mail list about the python wrapper for the xdrfile library: http://oldwww.gromacs.org/pipermail/gmx-developers/2009-March/003176.html But unfortunately the link for the python files are not valid anymore. I am wondering whether this proj

Re: [gmx-users] Learning MD

I suggest you start at http://manual.gromacs.org/current/online/flow.html There are two other links: 1. http://nmr.chem.uu.nl/~tsjerk/course/molmod/ 2. http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao

Re: [gmx-users] Learning MD

sonali dhindwal wrote: Hello All, I am new at MD, and i have started doing it few months ago only. I tried to run some simulations but taking all the parameters using some tutorials given online and have not got very good results. Can someone please help in suggesting what is the best way to

Re: [gmx-users] Learning MD

Hello, Providing information on what type of simulations you'll be running, what you hope to accomplish with MD, and what analysis tools you expect to use might allow others to better help you :) --Venk On Mon, May 10, 2010 at 12:57 PM, sonali dhindwal < sonali11dhind...@yahoo.co.in> wrote: > H

[gmx-users] Learning MD

Hello All, I am new at MD, and i have started doing it few months ago only. I tried to run some simulations but taking all the parameters using some tutorials given online and have not got very good results. Can someone please help in suggesting what is the best way to learn MD using Gromacs i

[gmx-users] PMF of ligand transport

Pick a small collection of backbone atoms near the center of your channel and use them as your reference group. Overcome the sign problem by optimal selection of pull options (see below). pull_pbcatom values should not be important if you select your groups as I suggest -- otherwise be sure to un

[gmx-users] Re: PMF of ligand transport

I think Justin meant that you have various positions of the ligand in the channel (from the SMD), so you don't need to make a new run to determine new positions in the channel. You need only new umbrella sampling simulations. Yep, the movement of the particle will also matter, because if the

Re: [gmx-users] Re: PMF of ligand transport

Justin A. Lemkul wrote: Aswathy wrote: Hi Justin, I am sorry, i dint understand this point "Your problem was only related to the actual umbrella sampling itself." ? You meant I just want to repeat umbrella sampling only? Yes. The manner in which you generate the initial configuration

Re: [gmx-users] Re: PMF of ligand transport

Aswathy wrote: Hi Justin, I am sorry, i dint understand this point "Your problem was only related to the actual umbrella sampling itself." ? You meant I just want to repeat umbrella sampling only? Yes. The manner in which you generate the initial configurations on which you will conduc

Re: [gmx-users] naive question about the c-terminus

abdullah ahmed wrote: The gromacs version is 3.3.1, which I am using on cygwin in the windows enviroment. Any particular reason you're using software that is over four years old? There are numerous bug fixes and performance enhancements in the 4.0.x series (with 4.0.7 being the newest).

[gmx-users] PMF of ligand transport

Don't use a dummy particle for your PMF if you can avoid it and test it thoroughly if you must use it. In my own work, I have received what appears to be erroneous results when using a dummy atoms together with dihedral restraints and the pull code. In my case I was actually using a dummy atom

RE: [gmx-users] naive question about the c-terminus

Perhaps I should also add that the N-terminus is working fine. I have two hydrogen molecules bound to the nitrogen on the N-terminus, and Gromacs can read that fine. I can also ask it to make the terminus NH3, and that works fine too. > Date: Mon, 10 May 2010 11:00:06 -0400 > From: jalem...@vt

Re: [gmx-users] Re: PMF of ligand transport

Hi Justin, I am sorry, i dint understand this point "Your problem was only related to the actual umbrella sampling itself." ? You meant I just want to repeat umbrella sampling only? In order to further understand that "Distance " problem, May I ask one more question,( please ignore if its a stupi

RE: [gmx-users] naive question about the c-terminus

The gromacs version is 3.3.1, which I am using on cygwin in the windows enviroment. The command I used is: "pdb2gmx -f test.pdb -p test.top -o test.gro -ter" and the forcefield is Encad all- atom forcefield, using scaled down vacuum charges. > Date: Mon, 10 May 2010 11:00:06 -0400 > From: jal

[gmx-users] Re: PMF of ligand transport

Would it be possible to use a dummy particle near the entrance of the channel? = is the channel and x the dummy and l the ligand x l = later time x ==l== Give the dummy no charge and zero lj-parameters and construt the position form the atoms at the entry of the channel. I think it will be

Re: [gmx-users] naive question about the c-terminus

abdullah ahmed wrote: I'm sorry I should have been more clear. Because the PDB file starts from residue number 23, the residue labelled 44 in the PDB is the residue that the error message refers to. Actually there is no residue 22 in the PDB file. You are also somewhat correct in saying tha

Re: [gmx-users] PMF of ligand transport

Aswathy wrote: Thank you very much for all replies. No w I just want to try SMd with geometry type as position . But one thing is still confusing me, ie; reference group. If you have already generated a suitable set of positions from which you have generated umbrella sampling windows, y

RE: [gmx-users] naive question about the c-terminus

I'm sorry I should have been more clear. Because the PDB file starts from residue number 23, the residue labelled 44 in the PDB is the residue that the error message refers to. Actually there is no residue 22 in the PDB file. You are also somewhat correct in saying that there are more than one

Re: [gmx-users] naive question about the c-terminus

abdullah ahmed wrote: Hello everyone! I have a naive question and I have been trying to find a solution myself, but I just don't understand what is wrong. When I run pdb2gmx with "-ter" on my molecule I get the following error message when I ask for a COOH to be made at the C terminus (I g

Re: [gmx-users] naive question about the c-terminus

On May 10, 2010, at 4:12 PM, abdullah ahmed wrote: Hello everyone! I have a naive question and I have been trying to find a solution myself, but I just don't understand what is wrong. When I run pdb2gmx with "-ter" on my molecule I get the following error message when I ask for a COOH to

Re: [gmx-users] MARTINI protonated histidine

I am trying to set up a simulation of a protein with the MARTINI force field. Two of the histidines in the protein are judged to be protonated and thus charged. This histidine is not described in the MARTINI force field as far as I can tell? No there is no parameters for charged histidines

Re: [gmx-users] ELNEDIN disulfide bridge

the force constant in MArtini is 5000 kJ/mol/nm^2 On May 10, 2010, at 4:21 PM, XAvier Periole wrote: There no specific term associated with di-sulfide bridge in ElNeDyn. It is however recommended to use a cutoff for the Elastic network of 0.9 nm. The two Backbone beads are certainly within

Re: [gmx-users] ELNEDIN disulfide bridge

There no specific term associated with di-sulfide bridge in ElNeDyn. It is however recommended to use a cutoff for the Elastic network of 0.9 nm. The two Backbone beads are certainly within that distance so it is pretty save. Nevertheless to include the disulfide bridge explicitly you shou

Re: [gmx-users] Re: configure error

Hi Lina, I am sorry to ask you about this again but I am having trouble finding the post you mentioned: gmx-users Digest, Vol 72, Issue 18. I ran autoreconf but it didn't work. Do you have to use version 2.13 or just any version later than 2.13. I ran version 2.61 and I am wondering if that was

[gmx-users] naive question about the c-terminus

Hello everyone! I have a naive question and I have been trying to find a solution myself, but I just don't understand what is wrong. When I run pdb2gmx with "-ter" on my molecule I get the following error message when I ask for a COOH to be made at the C terminus (I get no error when I ask

[gmx-users] MARTINI protonated histidine

I am trying to set up a simulation of a protein with the MARTINI force field. Two of the histidines in the protein are judged to be protonated and thus charged. This histidine is not described in the MARTINI force field as far as I can tell? I thought I could modify my way out of it by simp

[gmx-users] ELNEDIN disulfide bridge

I am trying to set up an ELNEDIN simulation of a protein which contain a disulfide bridge. As all the bonded interactions are changed compared to the MARTINI force field, I do not know how the parameters should be set for this bond, as it would seem unreasonable simply to use the MARTINI va

Re: [gmx-users] PMF of ligand transport

Using a flexible reference to generate a PMF is certainly not a good idea. More than affecting your convergence, your distance may have only little to do with the actual position of your ion in the channel. Imagine the ion is in a stable position and has to go over some energy barrier. It l

Re: [gmx-users] rigid or flexible water models

It is important to add that none f the current model (TIP3P and SPC) have been parameterized to be used as flexible. The Flexible option used for minimization if necessary. Using flexibility for both the HOH angle and the OH bonds will result in a different model and as far as I know it will

[gmx-users] PMF of ligand transport

Dear Aswathy: While not technically incorrect, it will make convergence much more difficult and is probably realistically incorrect given today's cpu power. But then again perhaps you have some particularly important reason to make that choice. In the absence of that, find some atom(s) th

Re: [gmx-users] rigid or flexible water models

shahab shariati wrote: Dear Justin application of SETTLE algorithm is equal to rigidity. is it true? thanks That would be the implication. If it's not flexible, it's rigid. And if it's rigid, then the SETTLE constraint algorithm is being applied to it. -Justin -- =

Re: [gmx-users] PMF of ligand transport

Aswathy wrote: On Mon, May 10, 2010 at 6:29 PM, Justin A. Lemkul > wrote: Ok . Now I understood. I have one more doubt , as I mentioned to you, I am using one residue in the extracellular loop as a reference point. Since this is in the loop, do you think

Re: [gmx-users] PMF of ligand transport

On Mon, May 10, 2010 at 6:29 PM, Justin A. Lemkul wrote: > Ok . Now I understood. I have one more doubt , as I mentioned to you, I am > using one residue in the extracellular loop as a reference point. Since this > is in the loop, do you think it can be good reference point (due to th large > flu

[gmx-users] rigid or flexible water models

Dear Justin application of SETTLE algorithm is equal to rigidity. is it true? thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe r

Re: [gmx-users] PMF of ligand transport

Aswathy wrote: I am pulling through the channel with respect to a single residue on one "side"(extracellular) of the structure. I have used pull_geometry = distance & pull_dim = N N Y. From this what I understood is ligand will pull along the z direction with respect to the reference group

Re: [gmx-users] rigidn or flexible water models

shahab shariati wrote: Hi gromacs users Is TIP3P water model rigid? It can be. rigidity means deletion of bonded interactions. is it true? No. Deletion of bonded interactions means you don't have an intact molecule! Have a look at the "#ifdef FLEXIBLE" block in the tip3p.itp file.

Re: [gmx-users] error in hydrocarbon dihedrals of opls-aa?

Am 07.05.2010 16:03, schrieb David van der Spoel: On 5/7/10 8:45 AM, Markus Tusch wrote: Hi everybody, I've just compared the following opls-aa torsional parameters for hydrocarbons given in J. Comp. Chem., Vol. 18, No. 16, 1955 - 1970 (1997) as well as in J. Comp. Chem., Vol. 23, No. 15, 141

Re: [gmx-users] PMF of ligand transport

I am pulling through the channel with respect to a single residue on one "side"(extracellular) of the structure. I have used pull_geometry = distance & pull_dim = N N Y. From this what I understood is ligand will pull along the z direction with respect to the reference group (away from r_57). (i

Re: [gmx-users] PMF of ligand transport

Aswathy wrote: Thanks for your reply. In this case reference (r57) is not the part of the channel. But it is a residue in the loop above the channel entry. Thats why I used pull_geometry=distance. Therefore I am pulling the ligand away from this reference. So you are not pulling throu

Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ

Dear Tsjerk, No the problem was not with GROMACS. I have one structure as a X-ray and the other i created by homology modeling based on this structure. So the difference arose because my starting structures themselves were different. I did try trjconv with an index file , but it did not work ou

Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ

Hi Nahren, You can do that using trjconv and an index file with the atom indices as they are in the order as they have to be. But is that really your problem? To understand what happened, it would help if you gave the series of commands that led to these results. Cheers, Tsjerk On Mon, May 10,

Re: [gmx-users] PMF of ligand transport

Thanks for your reply. In this case reference (r57) is not the part of the channel. But it is a residue in the loop above the channel entry. Thats why I used pull_geometry=distance. Therefore I am pulling the ligand away from this reference. Thanks -Aswathy On Mon, May 10, 2010 at 3:05 PM, Tho

[gmx-users] Trj conversion: ABCXYZ to AXBYCZ

Dear Gromacs Users, I simulated two homologous (proteins) , and noticed after the simulation that in one trajectory, the protein is stored as ABCXYZ and in another it is as AXBYCZ. (where A, Z are chain information, ABC is a trimer and XYZ

Re: [gmx-users] PMF of ligand transport

Hi, If you defined the reference (r_57) as part of your channel then with pull_geometry=distance you will have problems as the distance between pull_group1 and pull_group0 becomes closer to zero and then the distance becomes positive again. I recently had this with my umbrella sampling simul

[gmx-users] rigidn or flexible water models

Hi gromacs users Is TIP3P water model rigid? rigidity means deletion of bonded interactions. is it true? Thank you so much for any help! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/sear