[gmx-users] centering molecule in the water box
Hi all, During my MD the molecule experience a drift. Now I want to put the molecule at the center of the water box. I tried with trjconv using the -pbc mol and -center flag and using a reference frame where the molecule is at the center of the box. It seems that all the box (water+molecule) is translated, and so the position of the molecule relatively to the box is unchanged. I also checked the gmx-users list and I didn't get any useful suggestion. Fabio ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Save all MD snapshot
Dear Users. Greetings. Please someone can tell me how can I proceed to save all MD snapshot for a long time simulation after equilibration. Thanks a lot for all. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Save all MD snapshot
Collins Nganou skrev: Dear Users. Greetings. Please someone can tell me how can I proceed to save all MD snapshot for a long time simulation after equilibration. You can set the parameters below to the value 1 in the configuration file for mdrun. nstxout = 1 nstvout = 1 nstfout = 1 /Andreas ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Save all MD snapshot
The snapshots are saved automatically during the simulation in the trajectory, e.g. mdrun ... -x trajectory.xtc How often snapshots are saved depends on the settings in your .mdp-file. I recommend some reading of the manual before starting any simulations. Regards Andreas From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Collins Nganou Sent: 01 July 2008 10:14 To: gmx-users@gromacs.org Subject: [gmx-users] Save all MD snapshot Dear Users. Greetings. Please someone can tell me how can I proceed to save all MD snapshot for a long time simulation after equilibration. Thanks a lot for all. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error with polymer surface modeling
h a wrote: Dear users, I'm working on simulating protein interactions with polymer surface for tissue engineering applications. I have developed a primitive model of polymer surface of polystyrene using genconf. I have obtained .gro and .itp files using prodrg. But now I face error when I use grompp though I included the .itp in .top file! It says atomtype CR61 is not found. Now I'm struck at this point from many days. So where would one go to find an atomtype? If you were to enter your $GMXLIB directory and 'grep CR61 *' it will print out all the occurrences of this atom type. It will tell you what force field it belongs to and what the atom type is. -Justin Is it that I should add atom types to the ffG43a1nb.itp and ffG43a1bon.itp ? But then where should I get different parameters. Thank you for your help. Harshith Asuri, 3rd year UG student IIT Kanpur, http://home.iitk.ac.in/~harshith http://home.iitk.ac.in/%7Eharshith ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] centering molecule in the water box
On Tuesday 01 July 2008 10:17, Fabio Affinito wrote: if you have only one molecule in the box, and you are equilibrated, why would your molecule move around? A visualization problem? Can you center it with editconf maybe? Peyman Hi all, During my MD the molecule experience a drift. Now I want to put the molecule at the center of the water box. I tried with trjconv using the -pbc mol and -center flag and using a reference frame where the molecule is at the center of the box. It seems that all the box (water+molecule) is translated, and so the position of the molecule relatively to the box is unchanged. I also checked the gmx-users list and I didn't get any useful suggestion. Fabio ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Error with polymer surface modeling
On Tuesday 01 July 2008 07:48, h a wrote: what is the error? Dear users, I'm working on simulating protein interactions with polymer surface for tissue engineering applications. I have developed a primitive model of polymer surface of polystyrene using genconf. I have obtained .gro and .itp files using prodrg. But now I face error when I use grompp though I included the .itp in .top file! It says atomtype CR61 is not found. Now I'm struck at this point from many days. Is it that I should add atom types to the ffG43a1nb.itp and ffG43a1bon.itp ? But then where should I get different parameters. Thank you for your help. Harshith Asuri, 3rd year UG student IIT Kanpur, http://home.iitk.ac.in/~harshith -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] centering molecule in the water box
The protein experience self-diffusion and so it moves through the simulation box. I tried also with editconf but the result is the same. F. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] centering molecule in the water box
Fabio Affinito wrote: Hi all, During my MD the molecule experience a drift. Now I want to put the molecule at the center of the water box. I tried with trjconv using the -pbc mol and -center flag and using a reference frame where the molecule is at the center of the box. It seems that all the box (water+molecule) is translated, and so the position of the molecule relatively to the box is unchanged. When prompted for a group to center, what are you choosing? It sounds like you've chosen 'System' if everything is moving. Try centering with respect to your molecule of interest. -Justin I also checked the gmx-users list and I didn't get any useful suggestion. Fabio ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] centering molecule in the water box
I choosed Protein for centering and System for output. Same stuff with editconf. F. Fabio Affinito, PhD email: [EMAIL PROTECTED] phone:+39 040 3787 303 fax:+39 040 3787 528 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] centering molecule in the water box
On Tuesday 01 July 2008 12:24, Fabio Affinito wrote: I think if it moves, then there is something more basic wrong, do you remove your center of mass motion appropriately? is your box homogeneously equilibrated? but if it does not move and it looks like as if it moved, then it's visual problem and not important! you could e.g. write something to cut the solvent molecules from one side and put them on the other side with some mapping dependant on your box type, if you would like to see your molecule at the center. btw, self diffusion is the diffusion of one molecule through others of its own kind, not through other molecules, solvent or else. if there is no chemical potential ( ~concentration ) difference, no mass transfer would take place. Peyman The protein experience self-diffusion and so it moves through the simulation box. I tried also with editconf but the result is the same. F. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] centering molecule in the water box
Peyman, the protein moves because the c.o.m. motion wasn't subtracted during the dynamics. On Tuesday 01 July 2008 12:24, Fabio Affinito wrote: I think if it moves, then there is something more basic wrong, do you remove your center of mass motion appropriately? is your box homogeneously equilibrated? but if it does not move and it looks like as if it moved, then it's visual problem and not important! you could e.g. write something to cut the solvent molecules from one side and put them on the other side with some mapping dependant on your box type, if you would like to see your molecule at the center. btw, self diffusion is the diffusion of one molecule through others of its own kind, not through other molecules, solvent or else. if there is no chemical potential ( ~concentration ) difference, no mass transfer would take place. Peyman Fabio Affinito, PhD SISSA/ISAS -Statistical and Biological Physics Via Beirut, 4 34014 Trieste ITALY email: [EMAIL PROTECTED] phone:+39 040 3787 303 fax:+39 040 3787 528 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Heme-O2 parameters
Dear All, I'm looking for gromacs parameters for heme bound to oxygen molecule . I will appreciate getting the parameters or any tip considering the best way to create them. Thank you Rotem Sertchook ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Partial Vs Formal Charges
Dear Gromacs USERs, My ligand, which contains a piperazine ring needs to be positively charged (+1). When I assign Gasteiger charges, it comes out to be -0.336 on the Nitrogen. But When I do a SEMI-EMPIRICAL PM3 to place my partial charge , it puts +0.733 on this atom. So does it mean it has put partial charge as (F.Charge - P. Charge). When I use InsightII (cff91 FF), the partial charge on this ligand was -0.556 and also it had a formal charge of +1. So kindly suggest me the best way out. Also, does gromacs takes formal charges automatically or is there a way to define the same. thanks nahren ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Heme-O2 parameters
If they are not among the user contributions, and if they are not published somewhere in the literature, you will have to derive them yourself (an advanced topic!). See here: http://wiki.gromacs.org/index.php/Parameterization And this one is probably applicable in your case, as well: http://wiki.gromacs.org/index.php/Exotic_Species -Justin Rotem Sertchook wrote: Dear All, I'm looking for gromacs parameters for heme bound to oxygen molecule . I will appreciate getting the parameters or any tip considering the best way to create them. Thank you Rotem Sertchook ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Partial Vs Formal Charges
nahren manuel wrote: Dear Gromacs USERs, My ligand, which contains a piperazine ring needs to be positively charged (+1). When I assign Gasteiger charges, it comes out to be -0.336 on the Nitrogen. But When I do a SEMI-EMPIRICAL PM3 to place my partial charge , it puts +0.733 on this atom. So does it mean it has put partial charge as (F.Charge - P. Charge). When I use InsightII (cff91 FF), the partial charge on this ligand was -0.556 and also it had a formal charge of +1. So kindly suggest me the best way out. The best way out is the one that you believe to be most defensible for your particular situation. I would suggest looking up some of the original references for force field derivations (OPLS, GROMOS, AMBER, etc.) to get a sense of what types of methods are typically employed in deriving parameters. If you can find similar functional groups that have already been parameterized, that would probably be a good resource. Also, does gromacs takes formal charges automatically or is there a way to define the same. Gromacs will assign charges to each atom based on what you provide in the .itp file. -Justin thanks nahren ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] segmentation fault
Dear users, Thanks a lot to Justin and a few others who really helped me in successfully running insulin. Now, I am trying to setup the input file for insulin with other enzyme and I am trying to merge the two chains of insulin. I am using the following command: pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb -inter -merge -ignh it is asking whether to merge (A B, BC). I allowed it to merge BC they are insulin chains and A is the rest of the enzyme. With the above command after adding all the protons to LYS etc.., it complains the folling: Segmentation fault: pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb -inter -merge -ignh It says like its creating the pdb and top files but nothing it could. The same command works fine if I remove -merge and its also worked well with insulin chains. I have enough space to run this too. Please let me know the suggestions. Ram. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] segmentation fault
The whole story continues to emerge... :-) You're probably experiencing this problem because you're trying to process two separate proteins with one pdb2gmx command. You will need to separate (i.e., using a text editor) chain A (whatever protein) from BC (insulin). Process them separately with pdb2gmx, using -merge with the insulin portion. What you'll have to do is then concatenate the output structure files (again, text editor or Unix 'cat' command), and include the insulin topology within the topol.top from Protein A. See Chapter 5 of the manual for more details on this, but it is essentially analogous to including a ligand topology (.itp) within a system topology (.top). -Justin rams rams wrote: Dear users, Thanks a lot to Justin and a few others who really helped me in successfully running insulin. Now, I am trying to setup the input file for insulin with other enzyme and I am trying to merge the two chains of insulin. I am using the following command: pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb -inter -merge -ignh it is asking whether to merge (A B, BC). I allowed it to merge BC they are insulin chains and A is the rest of the enzyme. With the above command after adding all the protons to LYS etc.., it complains the folling: Segmentation fault: pdb2gmx -f insu.pdb -p insu_p.top -o insu_p.pdb -inter -merge -ignh It says like its creating the pdb and top files but nothing it could. The same command works fine if I remove -merge and its also worked well with insulin chains. I have enough space to run this too. Please let me know the suggestions. Ram. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] tabulated potential both on pairs and non-bonded interactions / different cutoffs
Hello, trying to implement my force field into gromacs I have figured out that it is of vital importance to use diferrent cut-offs among different kind of atoms. I have 1-4 and 1-5 interactions with a set of epsilon and sigma parameters and the non bonded interactions (more than 4 bonds appart) with a different set. Every interaction among different type of atoms have different rvdw-switch and rvdw cutoffs. As a result I have to use a tabulated potential both for 1-4 and 1-5 interactions AND non-bonded interactions (1-6 and above). My question is how is it possible someone to do that in gromacs. How gromacs would be able to discern whether the interaction is 3 or 4 bonds appart OR more than 4 bonds? In case I cannot use tabulated potential for the interactions I'm interested in, could I keep the pair interactions as they are up to now under the pairs section and use at least tabulated potential for the non-bonded interactions? In any case of the above what would be the meaning of rvdw-switch and rvdw cutoffs in the mdp file? The number of different interactions I have are 6. Is it possible while tabulating the non-bonded interactions to have both energy and pressure correction? I have also seen that I can use reduced parameters (eplsilon and sigma) for all the non-bonded interactions, yet (correct me if I'm wrong) I do not think that this solves the problem of different cutoffs. That way only one interaction would have the correct cutoff. Unfortunately all my efforts up to now with one global cutoff don't bring the anticipated results. Thank you in advance, Nikos __ Gesendet von Yahoo! Mail. Dem pfiffigeren Posteingang. http://de.overview.mail.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_wham command issues
Hello, I am having trouble analyzing the XXX.pdo file output from my mdrun simulation using the g_wham command. Specifically, my command entered is: g_wham pull.pdo -o pull1.xvg The error given is: Opening file pull.pdo _ Program g_wham, VERSION 3.3.3 Source code file: gmx_wham.c, line 89 Fatal error: This does not appear to be a valid pdo file _ Motherhood Means Mental Freeze (The Breeders) I've looked into the gmx_wham.c file and found that line 89 corresponds to: if(strcmp(Buffer1,UMBRELLA)) fatal_error( 704 ,This does not appear to be a valid pdo file); I'm not sure of what this means. I've noticed that others have had this issue in the past, and am hoping someone has found my mistake. Formatting of my .pdo file maybe? If this is the case, can anyone provide sample .pdo file to compare with my own? Any help is appreciated. __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_wham command issues
I remember that at least for the old version of g_wham, you need to gzip the pdo files first. Lanyuan Lu Date: Tue, 1 Jul 2008 11:38:18 -0400 To: gmx-users@gromacs.org From: [EMAIL PROTECTED] Subject: [gmx-users] g_wham command issues Hello, I am having trouble analyzing the XXX.pdo file output from my mdrun simulation using the g_wham command. Specifically, my command entered is: g_wham pull.pdo -o pull1.xvg The error given is: Opening file pull.pdo _ Program g_wham, VERSION 3.3.3 Source code file: gmx_wham.c, line 89 Fatal error: This does not appear to be a valid pdo file _ Motherhood Means Mental Freeze (The Breeders) I've looked into the gmx_wham.c file and found that line 89 corresponds to: if(strcmp(Buffer1,UMBRELLA)) fatal_error( 704 ,This does not appear to be a valid pdo file); I'm not sure of what this means. I've noticed that others have had this issue in the past, and am hoping someone has found my mistake. Formatting of my .pdo file maybe? If this is the case, can anyone provide sample .pdo file to compare with my own? Any help is appreciated. __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi _ 新年换新颜，快来妆扮自己的MSN给心仪的TA一个惊喜！ http://im.live.cn/emoticons/?ID=18 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Abnormal popc struture after inserting protein
Hi all, I have embedded protein into POPC bilayer, I accomplished energy minimisation em.mdp file cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 500 ; Energy minimizing stuff ; emtol = 100 emstep = 0.01 nstcomm = 1.0 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.4 Tcoupl = no Pcoupl = no its showed following sentences Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 104 steps, but did not reach the requested Fmax 100. Potential Energy = -2.2754422e+05 Maximum force = 2.3355256e+03 on atom 913 Norm of force = 9.4749170e+03 gcq#191: These Gromacs Guys Really Rock (P.J. Meulenhoff) So I dont boughter about those sentences because I confirmed in list archives that I can proceed further steps and moreover em.gro file is fine, so I went for restrain, here I am getting abnormal POPC structure means POPC tails are tilting, water molecules structure also disturbed. Could you please tell me where iam doing mistake? my pr.mdp filetitle = protein in popc restrained define = -DPOSRES_protein constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 1; total 50 ps. nstcomm = 1 nstxout = 50 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.4 pbc = xyz ; Berendsen temperature coupling is on in three groups Tcoupl = Berendsen tc-grps = POPCProtein SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 310 310 310 ; Anisotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = anisotropic tau_p = 1.0 1.0 1.0 00 0 compressibility = 4.5e-5 4.5e-5 4.5e-5 00 0 ref_p = 1.0 1.0 1.0 00 0 ; Energy monitoring energygrps = POPC Protein SOL_CL- ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 310.0 gen_seed= 173529 Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Abnormal popc struture after inserting protein
minnale wrote: So I dont boughter about those sentences because I confirmed in list archives that I can proceed further steps and moreover em.gro file is fine, so I went for restrain, here I am getting abnormal POPC structure means POPC tails are tilting, water molecules structure also disturbed. Could you please tell me where iam doing mistake? Not really. You haven't told us much. What parameters are you using (for the protein and the lipids)? How did you insert your protein? Also realize that 50 ps is *extremely* short in the realm of membrane protein MD. Even after several hundred picoseconds things may look a bit strange. Prevailing wisdom is that between 25-30 ns of MD are required for the lipids to reach equilibrium (although they should look reasonable after just a few ns, but parameters like area per headgroup may not level off for a while). -Justin my pr.mdp filetitle = protein in popc restrained define = -DPOSRES_protein constraints= all-bonds integrator = md dt = 0.002; ps ! nsteps = 1; total 50 ps. nstcomm= 1 nstxout= 50 nstvout= 1000 nstfout= 0 nstlog = 10 nstenergy = 10 nstlist= 10 ns_type= grid rlist = 0.9 coulombtype= PME rcoulomb= 0.9 rvdw= 1.4 pbc= xyz ; Berendsen temperature coupling is on in three groups Tcoupl = Berendsen tc-grps= POPCProtein SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 310 310 310 ; Anisotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = anisotropic tau_p = 1.0 1.01.000 0 compressibility= 4.5e-5 4.5e-5 4.5e-5 00 0 ref_p = 1.0 1.01.000 0 ; Energy monitoring energygrps = POPC Protein SOL_CL- ; Generate velocites is on at 300 K. gen_vel= yes gen_temp= 310.0 gen_seed= 173529 Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: How to calculate dihedral angle ??
HI I use mk_angndx to produce angle.ndx then, enter g_angle -od angdist.xvg -ov angaver.xvg -type dihedral it follows the options: Group 0 (Phi=180.0_2_70) has 4 elements Group 1 (Phi=180.0_2_6) has16 elements Group 2 (Phi=180.0_2_40) has 192 elements Select a group: what does the file angle.ndx mean? what are the three groups represent ? which group should I pick up? this is the angle.ndx what does it mean?? [ Phi=180.0_2_70 ] 11121314 [ Phi=180.0_2_6 ] 7111213 911121312131415 12131417 [ Phi=180.0_2_40 ] 2 1 3 4 2 1 3 7 5 1 3 4 5 1 3 7 4 3 7 8 1 3 7 8 1 3 711 4 3 711 8 71112 3 711 9 8 711 9 3 71112 711 9 5 711 9101211 9 5 1211 91011 9 5 111 9 5 6 10 9 5 110 9 5 6 9 5 1 3 9 5 1 2 6 5 1 3 6 5 1 2 131415161314151917141516 171415191415192314151920 161519231615192015192321 151923242019232120192324 192321171923212224232117 242321222321171423211718 222117142221171821171415 211714131817141518171413 Thanks Lin Message: 2 Date: Mon, 30 Jun 2008 16:39:17 -0400 From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] How to calculate dihedral angle ?? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Chih-Ying Lin wrote: HI g_chi is designed to help user to calculate the dihedral angles. I have an organic compound and as the manual describes that .gro , .trr and ssdump.dat are the required input files to compute and collect the dihedral angles with time. g_chi is for use with the peptide backbone, according to the documentation, so I don't know how applicable it necessarily is to your situation. You might be better off using g_angle with an appropriate index group for the dihedral(s) of interest. I have had success using it with small organic molecules. -Justin For my case, .gro and .trr files are ready. How to prepare for ssdump.dat? Also, how do i tell gromacs the calculate the specific dihedral angles with time for me?? I did not fully understand the manual's description. thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: How to calculate dihedral angle ??
Chih-Ying Lin wrote: HI I use mk_angndx to produce angle.ndx then, enter g_angle -od angdist.xvg -ov angaver.xvg -type dihedral it follows the options: Group 0 (Phi=180.0_2_70) has 4 elements Group 1 (Phi=180.0_2_6) has16 elements Group 2 (Phi=180.0_2_40) has 192 elements Select a group: what does the file angle.ndx mean? I suggest reading the manual regarding index files. what are the three groups represent ? Whatever you told mk_angndx when you created the file. which group should I pick up? Whichever one(s) you want to analyze. -Justin this is the angle.ndx what does it mean?? [ Phi=180.0_2_70 ] 11121314 [ Phi=180.0_2_6 ] 7111213 911121312131415 12131417 [ Phi=180.0_2_40 ] 2 1 3 4 2 1 3 7 5 1 3 4 5 1 3 7 4 3 7 8 1 3 7 8 1 3 711 4 3 711 8 71112 3 711 9 8 711 9 3 71112 711 9 5 711 9101211 9 5 1211 91011 9 5 111 9 5 6 10 9 5 110 9 5 6 9 5 1 3 9 5 1 2 6 5 1 3 6 5 1 2 131415161314151917141516 171415191415192314151920 161519231615192015192321 151923242019232120192324 192321171923212224232117 242321222321171423211718 222117142221171821171415 211714131817141518171413 Thanks Lin Message: 2 Date: Mon, 30 Jun 2008 16:39:17 -0400 From: Justin A. Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] How to calculate dihedral angle ?? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Chih-Ying Lin wrote: HI g_chi is designed to help user to calculate the dihedral angles. I have an organic compound and as the manual describes that .gro , .trr and ssdump.dat are the required input files to compute and collect the dihedral angles with time. g_chi is for use with the peptide backbone, according to the documentation, so I don't know how applicable it necessarily is to your situation. You might be better off using g_angle with an appropriate index group for the dihedral(s) of interest. I have had success using it with small organic molecules. -Justin For my case, .gro and .trr files are ready. How to prepare for ssdump.dat? Also, how do i tell gromacs the calculate the specific dihedral angles with time for me?? I did not fully understand the manual's description. thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PME-User
Dear all, I have some questions concerning the usage of tables : 1. If one choose ' coloumbtype = User ' then GROMACS would calculate only the interaction according to the user specfied table within the specified cut off 'rcoloumb' and 'rlist'. The interaction beyond the cut offs would not be treaten according to the user specified potential. Is this right ? 2. When I set 'PME-User' then my question is how PME works together with coloumb potential functions specified in the table different from the 'normal' coloumb interaction : ~1/r. ? 3. What exactly means the statement of David : Added support for a combination of PME and USER determined coloumb potentials. The user has to take care that the combination of Coloumb and standard PME makes sense. (Mon Feb 7 ) Thank you for your time Sang Min ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_wham command issues
I've also tried to gzip the files, and subsequently use the same command line as below with the zipped file. Same problem. Any other ideas? On Tue, Jul 1, 2008 12:12 PM, LuLanyuan [EMAIL PROTECTED] wrote: I remember that at least for the old version of g_wham, you need to gzip the pdo files first. Lanyuan Lu Date: Tue, 1 Jul 2008 11:38:18 -0400 To: gmx-users@gromacs.org From: [EMAIL PROTECTED] Subject: [gmx-users] g_wham command issues Hello, I am having trouble analyzing the XXX.pdo file output from my mdrun simulation using the g_wham command. Specifically, my command entered is: g_wham pull.pdo -o pull1.xvg The error given is: Opening file pull.pdo _ Program g_wham, VERSION 3.3.3 Source code file: gmx_wham.c, line 89 Fatal error: This does not appear to be a valid pdo file _ Motherhood Means Mental Freeze (The Breeders) I've looked into the gmx_wham.c file and found that line 89 corresponds to: if(strcmp(Buffer1,UMBRELLA) fatal_error( 704 ,This does not appear to be a valid pdo file); I'm not sure of what this means. I've noticed that others have had this issue in the past, and am hoping someone has found my mistake. Formatting of my .pdo file maybe? If this is the case, can anyone provide sample .pdo file to compare with my own? Any help is appreciated. __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi _ ���껻���գױ���Լ���MSN�ǵ�TAһ��ϲ�� http://im.live.cn/emoticons/?ID=18 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Have read the manual = How to calculate dihedral angle??????
HI I have read the manual but the thing is that I could not get the answers from the manuals. So, I repeatly ask the same questions and if anyone could give me the exact answers. Thanks a lot. Lin I use mk_angndx to produce angle.ndx then, enter g_angle -od angdist.xvg -ov angaver.xvg -type dihedral it follows the options: Group 0 (Phi=180.0_2_70) has 4 elements Group 1 (Phi=180.0_2_6) has16 elements Group 2 (Phi=180.0_2_40) has 192 elements Select a group: what does the file angle.ndx mean? what are the three groups represent ? which group should I pick up? this is the angle.ndx what does it mean?? [ Phi=180.0_2_70 ] 11121314 [ Phi=180.0_2_6 ] 7111213 911121312131415 12131417 [ Phi=180.0_2_40 ] 2 1 3 4 2 1 3 7 5 1 3 4 5 1 3 7 4 3 7 8 1 3 7 8 1 3 711 4 3 711 8 71112 3 711 9 8 711 9 3 71112 711 9 5 711 9101211 9 5 1211 91011 9 5 111 9 5 6 10 9 5 110 9 5 6 9 5 1 3 9 5 1 2 6 5 1 3 6 5 1 2 131415161314151917141516 171415191415192314151920 161519231615192015192321 151923242019232120192324 192321171923212224232117 242321222321171423211718 222117142221171821171415 211714131817141518171413 Thanks Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
