Re: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1
>This sounds very much like something we should >fix. Can you file a bug report >at >https://redmine.gromacs.org/ where you can also >upload the file that you >are trying to run? Let me >know if you have any trouble with uploading the >>report - I'm eager to know what happened. Best, >Christian I had reported >this bug in few days ago, please see this link: >https://redmine.gromacs.org/issues/3444 Thanks Yujie Liu -- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs binaries for windows (Cygwin 64)
It is great! But, I think more effective is to enable CUDA (GPU) support. https://www.dropbox.com/s/jtk5p7bz0ppgcbf/windows_gromacs2019.3%2Bfftw%2BintelC%2B%2B%2Bcuda10.rar?dl=0 here is a CUDA version of GROMACS 2019.3 by using VS 2017 and Intel C++, which is support AVX2_256 and more effective because it can use your GPU. More compile informations can been found my own wesit https://liuyujie714.com/15.html YuJie Liu -- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PMF wrong when calculating dihedral angle rotate
Dear gmx users, I want to repeat a amber tutorial *http://ambermd.org/tutorials/advanced/tutorial17/index.htm <http://ambermd.org/tutorials/advanced/tutorial17/index.htm>* by using gromacs, which is about PMF calculation of Alanine Dipeptide Phi/Psi Rotation. Everything is ok about the process of simulation, firstly equilibrium and generate a series of configuration, then do long simulation respectively. However, When using "gmx whan -it tpr.dat -if/x pullf/x.dat -cycl" command to generate PMF curve, I found histo.xvg figure is very good but profile.xvg figure is wrong. Then I check the data of profile.xvg file, found the second column data is "-nan". I also assign -min and -max, but still wrong. Finally, I found same question on the internet, the URL is *https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-August/108093.html <https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-August/108093.html>* and *https://redmine.gromacs.org/issues/2609 <https://redmine.gromacs.org/issues/2609>* . At the same time, I repeat this a sample PMF (*https://redmine.gromacs.org/attachments/2405/gwham_error_sample.tar.gz <https://redmine.gromacs.org/attachments/2405/gwham_error_sample.tar.gz>*) about angle by "gmx wham", I also found "profile.xvg" is wrong. I use GROMACS 2019.3. I hope some expert can give me some good advice. Whether the gromacs software can not generate correct PMF of angle? Thank you, YUjie Liu -- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Windows10+Visual studio 2017+CUDA8.0+Gromacs-2016.4
he file contains a character that cannot be represented in the current code page (936). Save the file in Unicode format to prevent data loss3>resource-division.cpp I don't know whether my operation is correct?? Besides, I built windows gromacs is based on this website mentioned (https://www.researchgate.net/post/I_need_to_install_GROMACS_on_windows_10_64_bit_system_Can_anyone_help_me_with_a_step_by_step_tutorial). My GPU is GTX950m belongs to notebook, which is not support "sm_20"Thanks again,Yujie Liu -- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Windows10+Visual studio 2017+CUDA8.0+Gromacs-2016.4
e contains a character that cannot be represented in the current code page (936). Save the file in Unicode format to prevent data loss3>resource-division.cpp I don't know whether my operation is correct?? Besides, I built windows gromacs is based on this website mentioned (https://www.researchgate.net/post/I_need_to_install_GROMACS_on_windows_10_64_bit_system_Can_anyone_help_me_with_a_step_by_step_tutorial). My GPU is GTX950m belongs to notebook, which is not support "sm_20"Thanks again,Yujie Liu -- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Windows10+Visual studio 2017+CUDA8.0+Gromacs-2016.4 package
Hello,every one; Now, I am trying to build a windows version of gromacs with CUDA8.0. In deed, according to some information from GROMACS official website and other experience, and I have already built some version of gromacs 5.1.x and its GPU version or 2016.x with CPU. However, I meet some error messages while using CUDA to build 2016.x-gromacs by Visual studio 2017 and intel MKL and cmake packages,etc. In detail error shows following:"E:/User-software/gromacs-2016.4/src\gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_fermi.cuh(406): error : identifier "c_oneSixth" is undefined in device code 2>" and "E:/User-software/gromacs-2016.4/src\gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_fermi.cuh(406): error : identifier "c_oneTwelveth" is undefined in device code 2>". Besides, I checked this error by google,here ( https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2016-December/009424.html) website also asked this error message but no got correct solution. Please help me to solve this problem Thanks, Yujie Liu -- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] nstcomm < nstcalenergy
Hi， Firstly, you should confirm your gromacs version, gromacs 5.x certainly includes nstcalenergy options in .mdp file. So you must set nstcalenergy=1 while the default value is 10 in .mdp if you want to nstcomm=1. thanks -- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] umbrella sample Question
Thanks Justin, You are right. Your script might not be compatible with my system or software, I tried to use another python script from other people and showed a complete dat file. Thanks again Yours, Liu -- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] umbrella sample Question
Thanks Justin, What do you means? I have carried out gmx distance to calculate the COM distance between two groups one by one through the previous confxxx.gro by myself, however I never met some fail or warnings. Finally, it seems that I can calculate the distance from all confxxx.gro as well as your script and just didn’t extract the distance value completely to a text. Can I use a fast method to extract these value? Please look my summary_distances.dat file -- 0 0.507 1 0.499 2 0.500 3 0.512 4 0.505 5 0.497 6 0.516 7 0.499 8 0.509 9 0.506 10 0.510 11 0.508 12 0.504 13 0.513 14 0.505 15 0.506 16 0.502 17 0.506 18 0.505 19 0.498 20 0.506 21 0.501 22 0.501 23 0.503 24 0.510 25 0.503 26 0.507 27 0.510 28 0.504 29 0.516 30 0.516 31 0.511 32 0.515 33 0.516 34 0.519 35 0.517 36 0.514 37 0.517 38 0.515 39 0.517 40 0.509 41 0.514 42 0.517 43 0.520 44 0.508 45 0.522 46 0.519 47 0.517 48 0.510 49 0.503 50 0.515 51 0.506 52 0.507 53 0.507 54 0.503 55 0.516 56 0.524 57 0.506 58 0.522 59 0.510 60 0.510 61 0.523 62 0.517 63 0.512 64 0.512 65 0.502 66 0.517 67 0.515 68 0.522 69 0.512 70 0.509 71 0.511 72 0.512 73 0.515 74 75 0.507 76 0.514 77 0.515 78 0.515 79 0.508 80 0.512 81 0.515 82 0.512 83 0.521 84 0.523 85 0.525 86 0.521 87 0.526 88 0.529 89 0.539 90 0.532 91 0.530 92 0.525 93 0.528 94 0.540 95 0.538 96 0.531 97 0.532 98 99 0.536 100 0.543 101 0.531 102 0.550 103 0.542 104 105 0.534 106 0.537 107 0.547 108 0.542 109 0.547 110 0.550 111 0.562 112 0.572 113 0.575 114 0.573 115 0.569 116 0.586 117 0.586 118 0.568 119 0.583 120 0.580 121 0.600 122 123 0.583 124 0.578 125 0.593 126 0.587 127 0.595 128 0.611 129 130 0.616 131 132 0.623 133 0.622 134 0.629 135 0.633 136 0.633 137 0.648 138 0.640 139 0.633 140 0.643 141 0.630 142 0.636 143 0.651 144 145 0.665 146 0.685 147 148 0.697 149 0.724 150 0.728 151 152 0.732 153 0.753 154 0.757 155 0.760 156 0.758 157 0.765 158 0.783 159 0.799 160 161 0.865 162 163 0.877 164 0.883 165 0.887 166 167 0.914 168 0.917 169 170 171 0.942 172 0.955 173 0.986 174 0.993 175 0.989 176 1.018 177 1.048 178 179 1.067 180 181 182 183 184 1.132 185 1.119 186 1.127 187 188 189 190 1.237 191 192 1.289 193 1.347 194 195 196 1.395 197 1.432 198 199 200 201 1.719 202 203 1.828 204 205 1.961 206 1.980 207 208 209 210 2.089 211 2.111 212 2.114 213 2.152 214 2.168 215 216 217 2.217 218 2.214 219 2.239 220 2.271 221 222 223 224 225 226 227 228 2.489 229 230 2.536 231 2.553 232 233 2.625 234 2.667 235 2.692 236 2.693 237 238 239 2.773 240 2.765 241 2.764 242 2.772 243 2.769 244 2.771 245 246 247 2.897 248 2.886 249 2.917 250 2.978 251 2.977 252 253 254 3.014 255 3.021 256 257 3.021 258 3.034 259 3.052 260 3.075 261 3.114 262 3.138 263 3.173 264 265 266 3.101 267 3.124 268 3.127 269 3.137 270 3.149 271 3.160 272 3.165 273 3.186 274 3.200 275 276 3.212 277 3.212 278 3.201 279 3.234 280 3.262 281 3.264 282 3.269 283 3.243 284 285 3.249 286 3.284 287 3.301 288 3.286 289 3.290 290 3.332 291 3.344 292 3.323 293 3.281 294 3.295 295 296 3.384 297 3.389 298 3.396 299 3.414 300 301 3.440 302 303 3.435 304 3.458 305 3.484 306 3.520 307 3.526 308 3.542 309 3.543 310 3.549 311 3.568 312 3.567 313 3.597 314 3.574 315 3.583 316 3.596 317 3.589 318 3.576 319 320 3.572 321 3.538 322 3.563 323 3.574 324 3.582 325 3.608 326 3.642 327 3.661 328 3.717 329 3.718 330 3.713 331 3.725 332 3.740 333 3.741 334 3.759 335 3.768 336 3.797 337 3.807 338 3.838 339 3.857 340 3.867 341 3.888 342 3.881 343 3.890 34
[gmx-users] umbrella sample Question
Hello，gromacs user I am a novice, I met some problems when I do this tutorial to learn umbrella sample, at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html. I am using gromacs 5.1.4 and the summary_distances.dat file is not complete while carrying out ‘perl distances.pl’. Some values of distance between COM of Chain_A and Chain_B are empty and some distxxx.xvg files still existing. In fact, I checked out some distxxx.xvg and found which existed a value of distance but why these values can’t write into summary_distances.dat completely by commend ‘perl distances.pl’ ? There is someone met with the situation?? Thanks Yours Liu. -- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?
The .top file of protein has included itself all parameters, so now you only copy gly.gro into protein.gro and changed the number of atoms. Then using #include” ” lines to add gly.itp into protein.top in suitable position and changed [molecules] options to add the name and number of gly molecule. Note the information of posre_gly.itp. -- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] The small organic molecule occurred deformation during simulation
Mr Justin: I have tried to do energy minimization in this situation which only existing small molecule in water, I found the structure of organic molecule didn’t become distortions. I think the distortions of organic molecules are due to these stronger interactions between small molecules and enzyme, because there is a enzyme molecule in the previous simulation. Do you think this consideration is correct? In the case, do you think this phenomenon is normal? What’s more, I checked out the top file of small molecules and don’t find error and include the information of improper dihedrals. Thank you very much! Yours, Yujie liu -- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] The small organic molecule occurred deformation during simulation
-- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] The small organic molecule occurred deformation during simulation
Hello, users I’m a novice to study the gromacs program. Now I met some problems which the small molecule occurred deformation when energy minimization was performed. For example, the anthracene molecule became bent in the plane of C-rings, the same as phenol. I want to know whether the situation is normal? In addition, I employed gromos54a7.ff Yours sincerely Yujie liu -- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Thanks a lot！ In fact, I just can not confirm the value of pconc or nconc of the polar.mdp, namely under what conditions should I set “0” or “0.150”？ *Yours sincerely* *Yujie, liu* -- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Some problem about the process of calculating MM-PBSA binding free energy
Dear users; I met some problem when I calculated the binding free energy between protein and ligand by the g_mmpbsa program. I am sure that I had read the tutorials of its official website and some other related information, but I don’t know what should I set the value of pconc or nconc in the input parameter when I use the file of polar.mdp. The default value is 0.150. Also, I don’t add fixed concentration when I use gmx genion command by GROMACS program and only use -neutral option. Yours sincerely Yujie, liu -- 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://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
